Re: [Bioc-devel] Availability of DropletUtils on BBS for an experiment package

[Leonardo Collado Torres]

Thank you Jennifer! I just made that change on both release and devel.

https://github.com/LieberInstitute/spatialLIBD/commit/94048657dd0cf134b8e2347933e4302f75cec415

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
Assistant Professor, Department of Biostatistics
Johns Hopkins Bloomberg School of Public Health
855 N. Wolfe St., Room 385
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com



On Wed, Nov 29, 2023 at 12:17 PM Jennifer Wokaty
 wrote:
>
> Hi Leo,
>
> spatialLIBD is missing DropletUtils in Suggests in the DESCRIPTION. If you 
> add it there and bump the version, it will pass check.
>
> Jennifer Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> 
> From: Bioc-devel  on behalf of Leonardo 
> Collado Torres 
> Sent: Wednesday, November 29, 2023 9:11 AM
> To: Bioc-devel 
> Subject: [Bioc-devel] Availability of DropletUtils on BBS for an experiment 
> package
>
> * This email originates from a sender outside of CUNY. Verify the sender 
> before replying or clicking on links and attachments. *
>
> Hi BioC-devel,
>
> Do you know why DropletUtils is not available on bioc 3.18 for the
> BBS? I keep seeing errors about it at
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fdata-experiment-LATEST%2FspatialLIBD%2Fnebbiolo2-checksrc.html__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEqcixawg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765624428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=G3JE%2FgBKp137DCvhmhcREQb%2F4sG%2BBd0cZkjlJm1P034%3D=0
> (which is an Experiment package, not a Software one)
>
> Quitting from lines 178-193 [import_to_r] (TenX_data_download.Rmd)
> Error: processing vignette 'TenX_data_download.Rmd' failed with diagnostics:
> there is no package called 'DropletUtils'
> --- failed re-building ‘TenX_data_download.Rmd’
>
> At 
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDropletUtils.html__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fE7mWBMjo%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765635135%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=w2%2BOmrICIKKycrQtbt56gSs0mt9Bc536baQbFhY8nts%3D=0
>  ,
> I do see that all binaries and the source package are available.
>
> Thanks,
> Leo
>
>
> Leonardo Collado Torres, Ph. D.
> Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
> Assistant Professor, Department of Biostatistics
> Johns Hopkins Bloomberg School of Public Health
> 855 N. Wolfe St., Room 385
> Baltimore, MD 21205
> lcolladotor.github.io
> lcollado...@gmail.com
>
> ___
> Bioc-devel@r-project.org mailing list
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEoKb0iBw%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765640048%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=2HWrzvP60fFjOcb18vywyDZDaghU9rx1K%2FshsCVYrA8%3D=0

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[Bioc-devel] Availability of DropletUtils on BBS for an experiment package

[Leonardo Collado Torres]

Hi BioC-devel,

Do you know why DropletUtils is not available on bioc 3.18 for the
BBS? I keep seeing errors about it at
https://master.bioconductor.org/checkResults/3.18/data-experiment-LATEST/spatialLIBD/nebbiolo2-checksrc.html
(which is an Experiment package, not a Software one)

Quitting from lines 178-193 [import_to_r] (TenX_data_download.Rmd)
Error: processing vignette 'TenX_data_download.Rmd' failed with diagnostics:
there is no package called 'DropletUtils'
--- failed re-building ‘TenX_data_download.Rmd’

At https://bioconductor.org/packages/release/bioc/html/DropletUtils.html,
I do see that all binaries and the source package are available.

Thanks,
Leo


Leonardo Collado Torres, Ph. D.
Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
Assistant Professor, Department of Biostatistics
Johns Hopkins Bloomberg School of Public Health
855 N. Wolfe St., Room 385
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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[Bioc-devel] TREG git push request access

[Leonardo Collado Torres]

Hi bioc-devel,

Similar to my qsvaR email, can you give me git access to TREG? Louise
is still the primary maintainer, but I'm helping her here and there.

Thanks,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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[Bioc-devel] qsvaR git access update request

[Leonardo Collado Torres]

Hi BioC-devel,

Could you give access to Hédia Tnani (https://github.com/HediaTnani
from my team) and myself to push updates to qsvaR? Joshua M. Stolz is
no longer working at LIBD and is no longer maintaining qsvaR. Hédia
will take over maintenance duties, though I'll help her here and
there.

Hédia, from 
https://contributions.bioconductor.org/git-version-control.html?q=DENIED%20by%20fallthru#faq
you'll need to submit your information to
https://git.bioconductor.org/BiocCredentials/.

Thanks,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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Re: [Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files

[Leonardo Collado Torres]

Awesome, thanks to both of you for checking this!

Best,
Leo


On Thu, Mar 2, 2023 at 2:36 PM Hervé Pagès  wrote:
>
> and also:
>
>kjohnson:~ biocbuild$ curl -O
> https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/rtracklayer_1.58.0.tgz
>
>kjohnson:~ biocbuild$ tar zxf rtracklayer_1.58.0.tgz
>
>kjohnson:~ biocbuild$ nm rtracklayer/libs/rtracklayer.so | grep
> _ssl_security
>00059aa8 T _ssl_security
>0006dda0 T _ssl_security_cert
>0006df38 T _ssl_security_cert_chain
>0006deb8 t _ssl_security_cert_key
>0005800c t _ssl_security_default_callback
>
> which confirms that the Mac arm64 binary currently available in release
> got linked to openssl.
>
> H.
>
> On 02/03/2023 10:52, Jennifer Wokaty wrote:
> > Hi Leo,
> >
> > I discussed this with Herve who noticed that you're running rtracklayer on 
> > an M1 Mac, so he looked at 
> > https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/rtracklayer/kjohnson-buildbin.html.
> >  It's linking to the static libraries for libssl.a and libcrypto.a so that 
> > it can be used on machine without these libraries according to the 
> > following line
> >
> > clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> > dynamic_lookup -single_module -multiply_defined suppress 
> > -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o 
> > rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o 
> > R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o 
> > chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o 
> > ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o 
> > ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o 
> > ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o 
> > ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o 
> > ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o 
> > ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o 
> > ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o 
> > ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o 
> > ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o 
> > ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread 
> > /opt/homebrew/Cellar/openssl@3/3.0.5/lib/libssl.a 
> > /opt/homebrew/Cellar/openssl@3/3.0.5/lib/libcrypto.a 
> > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> > -Wl,CoreFoundation
> >
> >
> > We have not made any recent changes to these binaries but these are the 
> > first ones we made available for M1 Macs.
> >
> > Jennifer Wokaty (they/them)
> >
> > Waldron Lab at CUNY SPH
> > Bioconductor Core Team
> > 
> > From: Bioc-devel  on behalf of Leonardo 
> > Collado Torres 
> > Sent: Thursday, February 23, 2023 2:48 PM
> > To: Bioc-devel 
> > Subject: [Bioc-devel] Openssl is not available in netConnectHttps for 
> > importing remote BigWig files
> >
> > ***ATTENTION: This email came from an external source. Do not open 
> > attachments or click on links from unknown senders or unexpected emails.***
> >
> >
> > Hi Bioc-devel,
> >
> > recount had been failing in recent months at bioc-release and
> > bioc-devel. I finally had the time to dive into it, and eventually
> > that led to an error on rtracklayer that I reported at
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lawremi_rtracklayer_issues_83=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_=B-a7fuBFTYUWc0FdqCGxVp5IX_asMYsRZ1BAQeYsXmI=
> >  . Michael Lawrence
> > noticed that my R session information didn't show openssl being
> > loaded. In a message there, Michael speculated that maybe a change in
> > how the rtracklayer binaries were being built by Bioconductor could be
> > the source of the issue.
> >
> > Here's a small reprex for the error:
> >
> > library("GenomicRanges")
> > library("rtracklayer")
> > range <- GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
> > rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpn

[Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files

[Leonardo Collado Torres]

Hi Bioc-devel,

recount had been failing in recent months at bioc-release and
bioc-devel. I finally had the time to dive into it, and eventually
that led to an error on rtracklayer that I reported at
https://github.com/lawremi/rtracklayer/issues/83. Michael Lawrence
noticed that my R session information didn't show openssl being
loaded. In a message there, Michael speculated that maybe a change in
how the rtracklayer binaries were being built by Bioconductor could be
the source of the issue.

Here's a small reprex for the error:

library("GenomicRanges")
library("rtracklayer")
range <- GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw;,
selection = reduce(range), as = "RleList")

And here's the error output:

Error in seqinfo(con) : UCSC library operation failed
In addition: Warning message:
In seqinfo(con) :
  No openssl available in netConnectHttps for sciserver.org : 443
> traceback()
7: seqinfo(con)
6: seqinfo(con)
5: .local(con, format, text, ...)
4: import(FileForFormat(con), ...)
3: import(FileForFormat(con), ...)
2: 
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw;,
   selection = reduce(range), as = "RleList")
1: 
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw;,
   selection = reduce(range), as = "RleList")
> packageVersion("rtracklayer")
[1] ‘1.58.0’


I'm not sure what else I can do to help. As noted at
https://github.com/lawremi/rtracklayer/issues/83#issuecomment-1437585161,
recount / rtracklayer versions from BioC 3.11 do work with the same
links.

Thanks in advance.

Best,
Leo


Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

[Leonardo Collado Torres]

Thanks! This will also help me ^^ https://orcid.org/-0003-2140-308X

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com



On Mon, Oct 19, 2020 at 7:43 AM Manders-2, F.M.
 wrote:
>
> Yes, I’ll create a PR.
>
> From: Vincent Carey 
> Date: Monday, 19 October 2020 at 12:36
> To: "Manders-2, F.M." , bioc-devel 
> 
> Subject: Fwd: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
> forwarding to bioc-devel
> -- Forwarded message -
> From: Vincent Carey 
> mailto:st...@channing.harvard.edu>>
> Date: Mon, Oct 19, 2020 at 6:33 AM
> Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
> To: Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
> Cc: Alessandro Lussana via Bioc-devel 
> mailto:Bioc-devel@r-project.org>>
>
> looks like BiocCheck/checks.R:validID <- 
> grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid)
>
> has to change -- do you have time to determine the correct regex for this and 
> file a PR?
>
>
>
> On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
>  wrote:
> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t know 
> why I have an X there and not a number.
>
> From: Vincent Carey 
> mailto:st...@channing.harvard.edu>>
> Date: Monday, 19 October 2020 at 12:20
> To: "Manders-2, F.M." 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
> Cc: Alessandro Lussana via Bioc-devel 
> mailto:Bioc-devel@r-project.org>>
> Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
>  person("Freek", "Manders", email = 
> "f.m.mand...@prinsesmaximacentrum.nl<mailto:f.m.mand...@prinsesmaximacentrum.nl>",
>  role = c("aut"),
> comment = c(ORCID = "-0001-6197-347X")),
>
> is what I see in a current checkout.  is "X" at the end correct?  maybe there 
> is an encoding issue?
>
> On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
>  wrote:
> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
> for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on the 
> dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> The information in this e-mail is intended only for th...{{dropped:30}}

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[Bioc-devel] Rmd vignette failures

[Leonardo Collado Torres]

As I was about to hit send, I checked Slack and I found about
https://github.com/Bioconductor/BiocStyle/issues/78. If you are in the
same situation as me, that info will be useful =) + the info on Slack



Original email:



Hi bioc-devel,

Today I got a bunch of emails because most of my packages failed with
errors such as:

Quitting from lines 31-39 (derfinderHelper.Rmd)
Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics:
argument is of length zero

The error basically points to the first R chunk in the Rmd files like
at 
https://github.com/leekgroup/derfinderHelper/blob/master/vignettes/derfinderHelper.Rmd#L30-L39
for each vignette. I've noticed a similar error in the GitHub Actions
logs for a package I'm actively working on (macOS and Windows using R
from r-lib; Linux using bioc-devel docker still worked details at
https://github.com/LieberInstitute/megadepth/runs/1152833313).

Are you aware of any change to pandoc or markdown that might be
related to this issue? I don't see anything at rstudio/rmarkdown
https://github.com/rstudio/rmarkdown/issues?q=argument+is+of+length+zero.

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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[Bioc-devel] A pie in the sky idea/wish: DifferentialExpressionSummarizedExperiment clas

[Leonardo Collado Torres]

Hi,

The tidybulk [1] workshop yesterday and Sean Davis & Levi Waldron's &
Benjamin Haibe-Kains workshop [2] got me thinking today in the morning
of a pie in the sky idea. Just like SummarizedExperiment has helped
many of us to organize our data, it would be awesome if there was
something like a DifferentialExpressionSummarizedExperiment class or
something like that. I know that Andrzej Oleś did a lot of work in
DEFormats, and it seems like now the Stefano Mangiola & Maria Doyle
are going through a similar effort of adding support to both edgeR and
DESeq2 (and limma??) outputs. I went through something similar with
regionReport, and well, if there was a common output object type or
functions that converted the current outputs into a common format,
that might make building upon these tools (and other DE packages) much
easier. I bet that you could submit a CZI EOSS application for
supporting the refactoring process & defining the output format.

Though maybe you already tried doing this in the past and I'm simply
unaware of it. Anyway, just an idea/wish.

Best,
Leo

PS I'd post this on Slack, but I'm not sure everyone's active there.

[1] http://bioconductor.org/packages/release/bioc/html/tidybulk.html
and https://twitter.com/Bioconductor/status/1287855026627518464?s=20
[2] https://twitter.com/Bioconductor/status/1287764789586989057?s=20
[3] http://bioconductor.org/packages/release/bioc/html/DEFormats.html

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Re: [Bioc-devel] regutools: request to add more git push access

[Leonardo Collado Torres]

Thank you Nitesh =)

And hm... I missed a couple of words in my email subject. Oops :P

On Mon, Apr 27, 2020 at 11:18 AM Carmina Barjon  wrote:
>
> Hi Nitesh! Yes, this it's the email address I will be using 
> (car.bar...@gmail.com).
> Thank you
> Carmina
>
> El lun., 27 abr. 2020 a las 5:59, Nitesh Turaga () 
> escribió:
>>
>> Hi Leo,
>>
>> I've added you and Alejandro to the regutools package.
>>
>> Carmina and Emiliano, please confirm the email addresses you'll be
>> using. I can add you both as well, and create BiocCredentials accounts
>> for you.
>>
>>
>> Nitesh
>>
>> On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote:
>> > Hi Nitesh,
>> >
>> > Could you add me (l.collado-torres) and Alejandro Reyes (what's your
>> > svn username Alejandro?) to regutools' list of contributors that have
>> > git push access? I think this is what we are supposed to do from
>> > re-reading 
>> > https://github.com/Bioconductor/Contributions/issues/1393#issuecomment-597202057.
>> >
>> > Carmina & Emiliano might want git push access too, but they do not
>> > have BioC git accounts as far as I know.
>> >
>> > Anyway, for now, I just wanted to add two commits already on GitHub
>> > and push them to BioC's git repo following
>> > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>> > before BioC 3.11's freeze.
>> >
>> > Thanks,
>> > Leo
>> >
>> > ___
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>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

[Leonardo Collado Torres]

ternally (it includes also recommended packages though):
>
> deps <- remotes::local_package_deps(pkgdir = ".", dependencies = TRUE)
>
> I guess I would further simplify the problem by eliminating from 'deps' the 
> packages that do not contribute to the problem. So I wonder what a minimal 
> 'deps' looks like? This would be much more helpful for understanding the 
> problem than many 1000's of lines of output from CI.
>
>
> For my small example package, deps (as created with your code below) was just 
> TxDb.Hsapiens.UCSC.hg19.knownGene.
>
> So I conclude that the problem is actually IN BASE R, and that the fix is in 
> the incredibly complicated logic of install.packages.
>
>
> I’m going to agree with this :) just to try to get a bit further, I went 
> through the code of remotes, and in the end it comes down to calling 
> install.packages() with a certain list of packages, and a specified set of 
> repos (e.g. 
> https://github.com/r-lib/remotes/blob/5b3da5f852772159cc2a580888e10536a43e9199/R/install.R#L75).
>  So I tried to just install some packages with install.packages(), in an 
> empty library, to see what would happen. Experiments are here (not very 
> easily accessible, I admit, but still) if someone is interested: 
> https://github.com/csoneson/testinstall/actions
>
> Long story short, this works fine:
> > install.packages("TxDb.Hsapiens.UCSC.hg19.knownGene", repos = 
> > c(getOption('repos'), BiocManager::repositories()), type = "both", 
> > dependencies = TRUE)
>
> This doesn’t (tries to install annotation packages before GenomeInfoDbData):
> > install.packages(c("TxDb.Hsapiens.UCSC.hg19.knownGene","IRanges","GenomeInfoDb"),
> >  repos = c(getOption('repos'), BiocManager::repositories()), type = "both", 
> > dependencies = TRUE)
> With other combinations of packages, sometimes it works, sometimes not.
>
> At the same time, this works fine:
> > BiocManager::install(c("TxDb.Hsapiens.UCSC.hg19.knownGene","IRanges","GenomeInfoDb"))
>
>
> And one more observation which may or may not be related: locally, this fails 
> for me:
>
> > remotes::install_bioc('TxDb.Hsapiens.UCSC.hg19.knownGene')
>
> while this works:
>
> > remotes::install_bioc('SummarizedExperiment’)
>
> Charlotte
>
> On 27 Apr 2020, at 12:11, Martin Morgan  wrote:
>
> Personally, I wouldn't trust remotes to get the Bioconductor repositories, 
> and hence the dependency graph, correct. I say this mostly because of 
> problems to get BiocManager to get the repositories right during each phase 
> of the Biocoonductor release cycle, not to diss the remotes package.
>
> I'd grab the immediate dependencies ONLY of the new package from the 
> DESCRIPTION file (does remotes have a function to do this? I'd trust it to do 
> a better job than my hack, but I'd double check it)
>
>  dcf = read.dcf("DESCRIPTION", c("Depends", "Imports", "LinkingTo", 
> "Enhances", "Suggests"))
>  deps = unlist(strsplit(dcf, ",[[:space:]]*"))
>  deps = sub(" .*", "", deps)# no version info
>  deps = setdiff(deps, c("R", NA, rownames(installed.packages(priority = 
> "high"
>
> I'd then do the builds with
>
>  BiocManager::install(deps)
>
> If that failed and I wanted to 'peel back' a layer of responsibility to get 
> closer to a minimal reproducible example, I'd do
>
>  install.packages(deps, repos = BiocManager::repositories())
>
> I believe that (maybe you can confirm?) this fails for your case.
>
> BiocManager::repositories() is just a named character vector -- in devel it 
> is currently
>
> dput(BiocManager::repositories())
>
>  c(BioCsoft = "https://bioconductor.org/packages/3.11/bioc;,
>BioCann =   "https://bioconductor.org/packages/3.11/data/annotation;,
>BioCexp = "https://bioconductor.org/packages/3.11/data/experiment;,
>BioCworkflows = "https://bioconductor.org/packages/3.11/workflows;,
>CRAN = "https://cran.rstudio.com;)
>
> So I conclude that the problem is actually IN BASE R, and that the fix is in 
> the incredibly complicated logic of install.packages.
>
> I guess I would further simplify the problem by eliminating from 'deps' the 
> packages that do not contribute to the problem. So I wonder what a minimal 
> 'deps' looks like? This would be much more helpful for understanding the 
> problem than many 1000's of lines of output from CI.
>
> This might help to come up with a simple example to demonstrate Charlotte's 
> conclusion that the source packages are instal

[Bioc-devel] TxDb.Hsapiens.UCSC.hg19.knownGene fails to install unless you manually install GenomeInfoDbData first

[Leonardo Collado Torres]

Hi Bioc-devel,

Similar to the message I just sent about GenomicFeatures and
TxDb.Hsapiens.UCSC.hg19.knownGene, I found that
TxDb.Hsapiens.UCSC.hg19.knownGene will fail to install on both macOS
and Windows with a fresh R 4.0 and BioC 3.11 installation unless
GenomeInfoDbData is installed manually before.

At 
https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1192
you can see how it failed.

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
1193** using staged installation
1194** R
1195** inst
1196** byte-compile and prepare package for lazy loading
1197##[error]Error: package or namespace load failed for
'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]):
1198ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
1199* removing 'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
1200 there is no package called 'GenomeInfoDbData'
1201##[error]Error: package 'GenomeInfoDb' could not be loaded

Immediately afterwards GenomeInfoDbData does get installed
https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1203
(tibble gets installed just after GenomeInfoDbData).

If you install GenomeInfoDbData prior to attempting to install
TxDb.Hsapiens.UCSC.hg19.knownGene you do not get this error as seen in
https://github.com/leekgroup/derfinderPlot/actions/runs/87730429

TxDb.Hsapiens.UCSC.hg19.knownGene depends on GenomicFeatures, which
then depends on GenomeInfoDb. Maybe GenomicFeatures is the one missing
both the imports/depends on GenomeInfoDbData and tibble.


These issues with missing dependencies in the DESCRIPTION files likely
don't show up on the Bioconductor build machines since these packages
are installed already.

Best,
Leo

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[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

[Leonardo Collado Torres]

Hi Bioc-devel,

I think that there's a potential issue with either GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package.


On a fresh R 4.0 Windows installation with BioC 3.11, I get the
following error message when installing
TxDb.Hsapiens.UCSC.hg19.knownGene as shown at
https://github.com/leekgroup/derfinderPlot/runs/618370463?check_suite_focus=true#step:13:1225.


2020-04-25T18:32:26.0765748Z * installing *source* package
'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
2020-04-25T18:32:26.0769789Z ** using staged installation
2020-04-25T18:32:26.1001400Z ** R
2020-04-25T18:32:26.1044734Z ** inst
2020-04-25T18:32:26.2061605Z ** byte-compile and prepare package for
lazy loading
2020-04-25T18:32:30.7296724Z ##[error]Error: package or namespace load
failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc,
.libPaths()), versionCheck = vI[[i]]):
2020-04-25T18:32:30.7305615Z ERROR: lazy loading failed for package
'TxDb.Hsapiens.UCSC.hg19.knownGene'
2020-04-25T18:32:30.7306686Z * removing
'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
2020-04-25T18:32:30.7307196Z  there is no package called 'tibble'
2020-04-25T18:32:30.7310561Z ##[error]Error: package 'GenomicFeatures'
could not be loaded
2020-04-25T18:32:30.7311805Z Execution halted

>From looking at the bioc-devel landing pages for both GenomicFeatures
and TxDb.Hsapiens.UCSC.hg19.knownGene, I see that tibble is not listed
as a dependency for either package.

Best,
Leo

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Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

[Leonardo Collado Torres]

Hi,

This seems related
https://twitter.com/opencpu/status/1253649367946444802?s=21

Best,
Leo

On Wed, Apr 22, 2020 at 6:54 AM Gordon K Smyth  wrote:

> Hi Herve,
>
> > Are you saying that 'R CMD config CC' returns
> > /mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest
> > Windows build of R 4.1.0?
>
> No, it doesn't. I was just trying to interpret the note "This build of
> R-Devel uses the gcc gcc 8.3.0 toolchain from rtools40." that is attached
> to R-4.1.0 for Windows on the CRAN download page. There's no similar note
> attached to R-4.0.0 RC, but I may have jumped to the wrong conclusion.
>
> Gordon
>
> > -Original Message-
> > From: Hervé Pagès 
> > Sent: Tuesday, 21 April 2020 6:51 PM
> > To: Gordon K Smyth ; Martin Morgan
> > ; bioc-devel@r-project.org
> > Cc: Yunshun Chen 
> > Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
> >
> > On 4/20/20 23:28, Gordon K Smyth wrote:
> > > Thanks, that does help. So it seems that R-4.0.0 will use
> > >
> > >rtools40/mingw64/bin/gcc.exe
> > >
> > > and I'm guessing that R-4.1.0 uses
> > >
> > >rtools40/mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0.exe
> >
> > I didn't try R 4.1.0 yet so don't know what it uses but I'm surprised it
> > uses something different than R 4.0.0. Are you saying that 'R CMD config
> > CC' returns /mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest
> > Windows build of R 4.1.0?
> >
> > Anyway I still have 6 months to worry about what R 4.1.0 does ;-)
> >
> > Cheers,
> > H.
> >
> > >
> > > Both files in are in the same directory, so R-4.0.0 and R-4.1.0 should
> both work
> > with same Windows setup (which is afterall what the Rtools webpage says).
> > >
> > > Thanks
> > > Gordon
> > >
> > >> -Original Message-
> > >> From: Hervé Pagès 
> > >> Sent: Tuesday, 21 April 2020 2:55 PM
> > >> To: Gordon K Smyth ; Martin Morgan
> > >> ; bioc-devel@r-project.org
> > >> Cc: Yunshun Chen 
> > >> Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
> > >>
> > >> Yes, all builds of R 4.0 and above are now using Rtools40 on Windows.
> See:
> > >>
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-
> > 2Dproject.org_bin_windows_Rtools_=DwIGaQ=eRAMFD45gAfqt84VtBcfh
> > Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Lbl2W3r-
> > f_jIrRVzr8IFYC0x_V3F3tjiBkHuXyGBhWA=Os0nDoCIS80pkl11embl1PwAXrLmd
> > 7lV67FCUN2db-o=
> > >>
> > >> AFAIK there has been no official announcement about this on the
> various
> > >> R-* mailing lists but this is suggested by the output of 'R CMD config
> > >> CC' which has changed from C:/Rtools/mingw_64/bin/gcc to
> > >> /mingw64/bin/gcc with the most recent Windows builds of R 4.0.0.
> > >>
> > >> /mingw64/bin/gcc and /mingw32/bin/gcc are the paths to the 64-bit and
> > >> 32-bit compilers **in the Msys environment** that is shipped with
> > >> Rtools40. These paths are relative to the location of Rtools40, which
> by
> > >> default is C:\Rtools40.
> > >>
> > >> Hope this helps,
> > >> H.
> > >>
> > >>
> > >> On 4/20/20 19:38, Gordon K Smyth wrote:
> > >>> Hi Herve,
> > >>>
> > >>> Ah, I see now.
> > >>>
> > >>> I was getting confused by the CRAN page that points to R-4.1.0 for
> > Windows
> > >> and says it "will eventually become the next major release of R". I
> see now
> > that
> > >> we should be using R-4.0.0 RC instead, which is the patched link.
> > >>>
> > >>> Can I confirm whether we should be using Rtools3.5 or Rtools4.0 with
> R-
> > 4.0.0
> > >> RC for Windows? The release note for R-4.0.0 RC says that it was
> ported by
> > >> Guido Masarotto, Brian Ripley and Duncan Murdoch, which to me means it
> > must
> > >> be using the older toolchain. I had associated that toolchain in my
> mind with
> > >> Rtool3.5, but perhaps without any proper justification. Maybe
> Rtools4.0
> > >> supports both the 4.0.0 and 4.1.0 pipelines.
> > >>>
> > >>> Thanks
> > >>> Gordon
> > >>>
> >  -Original Message-
> >  From: Hervé Pagès 
> >  Sent: Tuesday, 21 April 2020 12:01 PM
> >  To: Gordon K Smyth ; Martin Morgan
> >  ; bioc-devel@r-project.org
> >  Cc: Yunshun Chen 
> >  Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs
> Rtools4.0
> > 
> >  Hi Gordon,
> > 
> >  The Bioconductor version to be released (BioC 3.11) uses R 4.0, not
> R
> >  4.1. The latest Windows built of R 4.0 is available on CRAN here:
> > 
> >   https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-
> > >>
> > 2Dproject.org_bin_windows_base_rpatched.html=DwIGaQ=eRAMFD45gAf
> > >>
> > qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=hj
> > >> 173hPUpLOLp7dFQ_16azQNCbeFfRPfQqgksa9-
> > >> 15s=H7efBWjbnmjHS7SQKjsjRlOG_7OvsT_Aq6rNUqJTK8c=
> > 
> >  Note that the upcoming devel version of Bioconductor (BioC 3.12)
> will
> >  still be based on R 4.0. We'll only start using R 4.1 for BioC 3.13.
> > 
> >  Cheers,
> >  H.
> > 
> > 
> >  On 4/20/20 17:42, 

Re: [Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

[Leonardo Collado Torres]

yihui/knitr/issues/1796#issuecomment-575371248
[3] 
http://leekgroup.github.io/regionReport/articles/regionReport.html#derfinder-single-base-level-case-1
[4] 
http://leekgroup.github.io/regionReport/reference/derfinderReport-example/basicExploration/basicExploration.html
[5] https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html
[6] https://github.com/Bioconductor/BiocStyle/issues?q=crop
[7] https://github.com/Bioconductor/BiocStyle/issues/65#issuecomment-552832630
[8] https://github.com/iSEE/iSEE/commit/817d24d0aa092d04cbdfeb5daf5bfe60a711435a
[9] 
https://github.com/leekgroup/regionReport/commit/14e7b714b7598add2b67d797668cecd121a726fe
[10] https://github.com/leekgroup/regionReport/runs/614073194#step:8:36
[11] 
https://github.com/leekgroup/regionReport/commit/c63ec2c737d8514f521ec64c66189ed8a8a772a2
[12] 
https://github.com/leekgroup/regionReport/runs/614135852?check_suite_focus=true#step:8:354
[13] 
https://github.com/leekgroup/regionReport/blob/c63ec2c737d8514f521ec64c66189ed8a8a772a2/inst/basicExploration/basicExploration.Rmd#L399
[14] 
https://github.com/leekgroup/regionReport/commit/c7b2fc8dc086befd0539a8425cab81cc61baeb02
[15] 
https://github.com/leekgroup/regionReport/runs/614159356?check_suite_focus=true#step:8:30
[16] https://gist.github.com/lcolladotor/73db141aea3c7d9540ecd18b9b253e40
[17] https://twitter.com/tslumley/status/1253505155523178496?s=20


On Thu, Apr 23, 2020 at 10:03 PM Leonardo Collado Torres

 wrote:
>
> Hi,
>
> I went to google again and maybe
> https://github.com/phw/peek/issues/112#issuecomment-296690302 is the
> answer? It would require someone with access to the Linux builder to
> check this particular ImageMagick config XML file.
>
> I had linked to this thread earlier
> https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
> though back then I mentioned that it could be a disk space issue. That
> was before the more recent thread about that ended with ggbio being
> bumpted to 1.35.2 (for which using Bioconductor's devel docker
> revealed the problem).
>
> I also just asked on Twitter
> https://twitter.com/fellgernon/status/1253502433231343617?s=20 to see
> if anyone has seen a similar error.
>
> Best,
> Leo
>
> On Thu, Apr 23, 2020 at 9:36 PM Leonardo Collado Torres
>  wrote:
> >
> > Hi Bioc-devel,
> >
> > I'm having trouble with my regionReport package on the Bioc-devel
> > (3.11) Linux builds. Two weeks ago, using the Bioconductor devel
> > docker I was able to reproduce an error that was solved by ggbio
> > bumping their version number to 1.35.2 as described in [1]. I've tried
> > my best to reproduce the error shown at [2] which is:
> >
> > Quitting from lines 224-229 (basicExploration.Rmd)
> > Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
> > R: unable to get registry ID `cache:hosts' @
> > error/registry.c/GetImageRegistry/202
> >
> > Recently [3], I bumped the regionReport version to 1.21.7 where I
> > explicitly asked for ggbio 1.35.2 to be available. I suspected that
> > the Linux builder still had version ggbio 1.35.1 installed. But that
> > did not resolve the issue as the current build report is for
> > regionReport version 1.21.7 and there's no error about ggbio 1.21.7
> > not being available. Hm... the required versions for the dependencies
> > does get checked at R CMD build (or even install), right?
> >
> > At [4] you can see that regionReport 1.21.7 can be successfully
> > checked against Bioconductor devel's docker. This uses GitHub actions
> > that has 7 GB of RAM available [5]. The memory resources (7GB vs 2.5
> > GB? [6]), disk space (14 GB vs ?) and some system dependencies are the
> > only differences I can think of (installed through [7], none seem to
> > me to be related from what I see at [8]) besides the Linux builder
> > differences vs the Bioconductor devel docker (dunno what they are).
> >
> > If you have any suggestions, please let me know.
> >
> > Best,
> > Leo
> >
> > [1] https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
> > [2] 
> > https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/regionReport/malbec2-buildsrc.html
> > [3] 
> > https://github.com/leekgroup/regionReport/commit/5e7d956f71011f8551f2431f5af0e212d04be9f1
> > [4] 
> > https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:8:98
> > [5] 
> > https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners#supported-runners-and-hardware-resources
> > [6] 
> > https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-605024369
> > 2.5 GB is used for the 32-bit windows Single Package Bui

[Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

[Leonardo Collado Torres]

Hi Bioc-devel,

I'm having trouble with my regionReport package on the Bioc-devel
(3.11) Linux builds. Two weeks ago, using the Bioconductor devel
docker I was able to reproduce an error that was solved by ggbio
bumping their version number to 1.35.2 as described in [1]. I've tried
my best to reproduce the error shown at [2] which is:

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202

Recently [3], I bumped the regionReport version to 1.21.7 where I
explicitly asked for ggbio 1.35.2 to be available. I suspected that
the Linux builder still had version ggbio 1.35.1 installed. But that
did not resolve the issue as the current build report is for
regionReport version 1.21.7 and there's no error about ggbio 1.21.7
not being available. Hm... the required versions for the dependencies
does get checked at R CMD build (or even install), right?

At [4] you can see that regionReport 1.21.7 can be successfully
checked against Bioconductor devel's docker. This uses GitHub actions
that has 7 GB of RAM available [5]. The memory resources (7GB vs 2.5
GB? [6]), disk space (14 GB vs ?) and some system dependencies are the
only differences I can think of (installed through [7], none seem to
me to be related from what I see at [8]) besides the Linux builder
differences vs the Bioconductor devel docker (dunno what they are).

If you have any suggestions, please let me know.

Best,
Leo

[1] https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
[2] 
https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/regionReport/malbec2-buildsrc.html
[3] 
https://github.com/leekgroup/regionReport/commit/5e7d956f71011f8551f2431f5af0e212d04be9f1
[4] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:8:98
[5] 
https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners#supported-runners-and-hardware-resources
[6] 
https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-605024369
2.5 GB is used for the 32-bit windows Single Package Builder.
[7] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:2
[8] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:167

Leonardo Collado Torres, Ph. D., Research Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
http://lcolladotor.github.io

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Re: [Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

[Leonardo Collado Torres]

Thanks Michael!

I verified that building regionReport works with ggbio 1.35.2
https://github.com/tengfei/ggbio/commit/6bc94f45e6479b01287e25140821f239f1a7f92d
on linux OS and I updated the gist at
https://gist.github.com/lcolladotor/b7585962082263b377c02fa4451f27e6
with a file linux_regionReport_build_ggbio_1.35.2.txt that has all the
relevant output. I also added a
linux_reprex_derfinderPlot_output_ggbio_1.35.2.txt that shows the
issues with validObject(hg19IdeogramCyto) from biovizBase.

My guess is that the linux OS had ggbio 1.35.1 from
https://github.com/tengfei/ggbio/commit/e385a446fc8a255515fbaba818ae59ef240d494f
that is one commit prior to
https://github.com/tengfei/ggbio/commit/930e521bfe0967f5095583c69f655fa571e3fa42
which fixes this issue and was maybe the ggbio 1.35.1 version I
installed on my macOS. This makes sense to me (and I'll keep a mental
note to check commit history in the future when OS reports differ),
but if have other possible explanations for the OS discrepancies
please let me know.

Thanks again for the speedy fix!! =)

Best,
Leo

On Thu, Apr 9, 2020 at 4:41 PM Michael Lawrence
 wrote:
>
> I bumped the version of ggbio which should propagate a recent fix.
>
> Michael
>
> On Thu, Apr 9, 2020 at 7:11 AM Leonardo Collado Torres 
>  wrote:
>>
>> Hi BioC-devel,
>>
>> I was able to trace a regionReport error back to ggbio & biovizBase.
>> However, I'm completely clueless as to why (a) it only appears in some
>> OS (though this has changed over time) and (b) it does not seem to be
>> a problem with derfinderPlot on the build reports for the same OS.
>>
>>
>>
>> ## Short version
>>
>> library('ggbio')
>> data(hg19IdeogramCyto, package = 'biovizBase')
>> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
>> tracks(p.ideo)
>>
>> This code on linux leads to 3 warnings from plotIdeogram() and an
>> error from tracks(). Also, validObject(hg19IdeogramCyto) fails (this
>> also fails on macOS).
>>
>> One warning (about seqlengths) and validObject() can be fixed with:
>>
>> hg19IdeogramCytoFixed <- updateObject(hg19IdeogramCyto)
>> seqlengths(hg19IdeogramCytoFixed) <-
>> seqlengths(getChromInfoFromUCSC('hg19', as.Seqinfo =
>> TRUE))[seqlevels(hg19IdeogramCytoFixed)]
>>
>>
>> This code is currently run from derfinderPlot::plotCluster() and for
>> some reason, the examples don't fail.
>>
>>
>>
>> ## Long version
>>
>> My package regionReport has been failing for a while with the same
>> error on Bioc-release (3.10) and bioc-devel (3.11). I've been watching
>> the fails for a while and it's mostly:
>>
>> * linux on 3.10, occasionally Windows
>> * linux on 3.11
>>
>> Right now, it's only linux on both 3.10 and 3.11.
>>
>> The error always is:
>>
>> Quitting from lines 224-229 (basicExploration.Rmd)
>> Error in magick_image_trim(image, fuzz) :
>>   R: unable to get registry ID `cache:hosts' @
>> error/registry.c/GetImageRegistry/202
>> Calls: render ...  -> assert_image ->  ->
>> magick_image_trim
>>
>>
>> A while back, I reported that I couldn't reproduce this on 3.10 on
>> Windows (when it was failing). I've looked at the magick package and
>> it didn't seem to be the issue
>> mhttps://github.com/ropensci/magick/search?q=magick_image_trim_q=magick_image_trim.
>>
>> After getting R 4.0.0 setup on my macOS, I also couldn't reproduce it.
>> So I finally looked at Nitesh's work on dockers at
>> http://bioconductor.org/help/docker/
>>
>>  docker run \
>>  -e PASSWORD=bioc \
>>  -p 8787:8787 \
>>  bioconductor/bioconductor_docker:devel
>>
>> There I could reproduce the build problem from regionReport and got a
>> more detailed error message. Using an interactive session where I ran
>> the internal code piece by piece, I got to the biovizBase + ggbio
>> error.
>>
>> derfinderPlot::plotCluster(), which is also a package I made, runs the
>> exact same code and has not failed at all on both bioc-release (3.10)
>> and devel (3.11) all this time. I would have expected derfinderPlot to
>> fail also (in which case it would have provided a more informative
>> error than the one hidden by rmarkdown in regionReport's build
>> reports). If I run the example for derfinderPlot::plotCluster() on
>> linux it does fail, however this was not picked up by the BioC build
>> report. Hence why I'm even more confused.
>>
>> Anyway, hopefully fixing the ggbio/biovizBase issue will fix
>> derfinderPlot::plotCluster() and in turn regionReport.
>>
>> As to the

[Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

[Leonardo Collado Torres]

Hi BioC-devel,

I was able to trace a regionReport error back to ggbio & biovizBase.
However, I'm completely clueless as to why (a) it only appears in some
OS (though this has changed over time) and (b) it does not seem to be
a problem with derfinderPlot on the build reports for the same OS.



## Short version

library('ggbio')
data(hg19IdeogramCyto, package = 'biovizBase')
p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
tracks(p.ideo)

This code on linux leads to 3 warnings from plotIdeogram() and an
error from tracks(). Also, validObject(hg19IdeogramCyto) fails (this
also fails on macOS).

One warning (about seqlengths) and validObject() can be fixed with:

hg19IdeogramCytoFixed <- updateObject(hg19IdeogramCyto)
seqlengths(hg19IdeogramCytoFixed) <-
seqlengths(getChromInfoFromUCSC('hg19', as.Seqinfo =
TRUE))[seqlevels(hg19IdeogramCytoFixed)]


This code is currently run from derfinderPlot::plotCluster() and for
some reason, the examples don't fail.



## Long version

My package regionReport has been failing for a while with the same
error on Bioc-release (3.10) and bioc-devel (3.11). I've been watching
the fails for a while and it's mostly:

* linux on 3.10, occasionally Windows
* linux on 3.11

Right now, it's only linux on both 3.10 and 3.11.

The error always is:

Quitting from lines 224-229 (basicExploration.Rmd)
Error in magick_image_trim(image, fuzz) :
  R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
Calls: render ...  -> assert_image ->  ->
magick_image_trim


A while back, I reported that I couldn't reproduce this on 3.10 on
Windows (when it was failing). I've looked at the magick package and
it didn't seem to be the issue
mhttps://github.com/ropensci/magick/search?q=magick_image_trim_q=magick_image_trim.

After getting R 4.0.0 setup on my macOS, I also couldn't reproduce it.
So I finally looked at Nitesh's work on dockers at
http://bioconductor.org/help/docker/

 docker run \
 -e PASSWORD=bioc \
 -p 8787:8787 \
 bioconductor/bioconductor_docker:devel

There I could reproduce the build problem from regionReport and got a
more detailed error message. Using an interactive session where I ran
the internal code piece by piece, I got to the biovizBase + ggbio
error.

derfinderPlot::plotCluster(), which is also a package I made, runs the
exact same code and has not failed at all on both bioc-release (3.10)
and devel (3.11) all this time. I would have expected derfinderPlot to
fail also (in which case it would have provided a more informative
error than the one hidden by rmarkdown in regionReport's build
reports). If I run the example for derfinderPlot::plotCluster() on
linux it does fail, however this was not picked up by the BioC build
report. Hence why I'm even more confused.

Anyway, hopefully fixing the ggbio/biovizBase issue will fix
derfinderPlot::plotCluster() and in turn regionReport.

As to the inconsistencies across OS or between the BioC build report
output for derfinderPlot and what I see on linux, I have no idea
though.


## Gist with details

I have a Gist with all the output logs and the R session information
at https://gist.github.com/lcolladotor/b7585962082263b377c02fa4451f27e6.
Here's the brief description for each file.

* macOS_regionReport_build.txt: runs R CMD build for regionReport
without a problem
* linux_regionReport_build.txt: fails to run R CMD build for
regionReport and provides more details and the BioC build report. This
is where we can start to see errors related to the ideograms. I
thought that fixing this would only involve a updateObject() call at
this point.
* reprex_ggbio_code.R: smallest code I have for reproducing this issue
* macOS_reprex_ggbio_output.txt: runs without errors (though it still
has warnings about seqlengths and other ggbio parts)
* linux_reprex_ggbio_output.txt: fails to run the small reprex
* reprex_derfinderPlot_code.R: runs the example for derfinderPlot::plotCluster()
* macOS_reprex_derfinderPlot_output.txt: similar story to
macOS_reprex_ggbio_output.txt:
* linux_reprex_derfinderPlot_output.txt: the example fails here too!
Which makes me even more confused. I mean, it's consistent with
regionReport and the ggbio reprex. However, I then don't understand
why this hasn't failed in the BioC builds.



Best,
Leo


Leonardo Collado Torres, Ph. D., Research Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
http://lcolladotor.github.io


On Tue, Mar 17, 2020 at 6:35 PM Leonardo Collado Torres
 wrote:
>
> Hi BioC-devel,
>
> I spent some time yesterday getting my Windows laptop ready to debug a
> Windows OS-only issue in regionReport (bioc-release 3.10), but
> ultimately I couldn't reproduce it. Since the error seems to be some
> type of cache, I bumped the version number but it still failed today
> and it then also failed on bioc-devel (3.11) on Linux (as well as
> Windows).
>
> ## Bioc-release (3.10)

[Bioc-devel] regionReport error: leads to potential disk space issues for ImageMagick

[Leonardo Collado Torres]

Hi BioC-devel,

I spent some time yesterday getting my Windows laptop ready to debug a
Windows OS-only issue in regionReport (bioc-release 3.10), but
ultimately I couldn't reproduce it. Since the error seems to be some
type of cache, I bumped the version number but it still failed today
and it then also failed on bioc-devel (3.11) on Linux (as well as
Windows).

## Bioc-release (3.10) Windows is the only that fails

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
--- failed re-building ‘regionReport.Rmd’

similarly

Quitting from lines 224-229 (basicExploration.Rmd)
Error in magick_image_trim(image, fuzz) :
  R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
Calls: render ...  -> assert_image ->  ->
magick_image_trim


## Bioc-devel (3.11) Linux and Windows fails

http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html

However, I see at
http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/malbec2-buildsrc.html
that the error appeared today also on the Linux bioc-devel builder.

## Google

Searching for the error message led me to
https://github.com/phw/peek/issues/112 which talks about disk space
running out for ImageMagick. Do you think that this is something that
is affecting the builders too? Do you have any suggestions I could
try?

Best,
Leo

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[Bioc-devel] [rOpenSci] Community Call: Maintaining an R Package

[Leonardo Collado Torres]

Hi BioC-devel,

Since 2018 I've been interacting with rOpenSci's organizers. For those
that don't know, rOpenSci https://ropensci.org/ is a non-profit that
aims to

> make scientific data retrieval reproducible. Over the past seven years we 
> have developed an ecosystem of open source tools, we run annual 
> unconferences, and review community developed software.

(taken from their https://ropensci.org/about/ page) That is, they are
in some ways similar to Bioconductor and that's why they want to build
a bridge between the two communities.

Stefanie Butland, their community manager, invited me to be a part of
a community call (webinar) on the topic of Maintaining an R Package in
order to bring in a little bit of the Bioconductor perspective. They
have a pretty nice system where they take questions before hand
through a GitHub issue page, so please feel free to chime in. I think
that besides the Bioconductor side, I bring in a bit of the CDSB
perspective (the work we do to help others in Mexico and Latin
America). In any case, feel free to tune in to the webinar (details
below) as well as share the information with anyone who might be
interested.

https://support.bioconductor.org/p/128869/

Best,
Leo

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Re: [Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis

[Leonardo Collado Torres]

Hi,

I should clarify that this workshop will be held in Cuernavaca,
Morelos, Mexico during August 3rd to the 7th, 2020.

Best,
Leo

On Thu, Mar 5, 2020 at 10:05 PM Leonardo Collado Torres
 wrote:
>
> Hi BioC-devel!
>
> We just made the announcement of our CDSB 2020 workshop at
> https://support.bioconductor.org/p/128868/ + Twitter & Facebook (both
> in English and Spanish). Joselyn and Rob will be among our
> instructors. Thank you Bioconductor Foundation for the support!
>
> Please help us spreading the word around. Also, if you have any
> contacts that you think might be interested in sponsoring the
> workshop, please let us know. At
> https://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer
> the question why should you support us? Thanks!
>
> Best,
> Leo
>
> Leonardo Collado Torres, Ph. D., Staff Scientist II
> Lieber Institute for Brain Development
> 855 N Wolfe St, Suite 300
> Baltimore, MD 21205
> Website: http://lcolladotor.github.io

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[Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis

[Leonardo Collado Torres]

Hi BioC-devel!

We just made the announcement of our CDSB 2020 workshop at
https://support.bioconductor.org/p/128868/ + Twitter & Facebook (both
in English and Spanish). Joselyn and Rob will be among our
instructors. Thank you Bioconductor Foundation for the support!

Please help us spreading the word around. Also, if you have any
contacts that you think might be interested in sponsoring the
workshop, please let us know. At
https://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer
the question why should you support us? Thanks!

Best,
Leo

Leonardo Collado Torres, Ph. D., Staff Scientist II
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io

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[Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages

[Leonardo Collado Torres]

Hi,

When installing BiocNeighbors (1.4.1, latest release from Bioconductor
version 3.10) from source on linux I noticed the issue as a few hours
ago it all worked fine but now it doesn't. Locally, I noticed that I
had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I
can install the BiocNeighbors 1.4.1 binary, I did the actual tests at
https://github.com/LTLA/BiocNeighbors/issues/10 and noticed that
RcppAnnoy's change lead to this. I have no idea how RcppAnnoy works,
but well, maybe if you use it in your package you do.

Now I need to google how to set on my DESCRIPTION to use the CRAN
archived version of RcppAnnoy 0.0.14 that you can install with

packageurl <- 
"https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz;
install.packages(packageurl, repos=NULL, type="source")
## From 
https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages

Best,
Leo

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Re: [Bioc-devel] Error unable to find image

[Leonardo Collado Torres]

Will do, thanks Lori!

Best,
Leo

On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Wait for knitr to be available on CRAN.
>
> The builders do not respect remotes to github repos.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ----------
> *From:* Bioc-devel  on behalf of
> Leonardo Collado Torres 
> *Sent:* Tuesday, January 21, 2020 1:19 PM
> *To:* Martin Morgan 
> *Cc:* Zach Shao ; bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> *Subject:* Re: [Bioc-devel] Error unable to find image
>
> Hi,
>
> Thanks for the links!
>
> Should we wait for the knitr fix to be available through CRAN or edit our
> DESCRIPTION files to force the Bioc machines to install `knitr` from
> GitHub?
>
> Best,
> Leo
>
> On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan 
> wrote:
>
> > This seems to be a problem with a recent change to knitr
> >
> >   https://github.com/Bioconductor/BiocStyle/issues/71
> >   https://github.com/yihui/knitr/issues/1797
> >
> > Please follow these issues; it looks like it is fixed in the github
> > repository, but needs to be made available in CRAN for this to be fixed
> on
> > our build systems.
> >
> > Martin
> >
> > On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" <
> > bioc-devel-boun...@r-project.org on behalf of zach.s...@gmail.com>
> wrote:
> >
> > Hello,
> >
> > Not sure what to make of this error
> >
> > with building the vingette by bioconductor.
> >
> > The figures are all there.
> >
> > Did something change with knitr?
> >
> > Thank you.
> >
> >
> > Zach
> >
> >
> >
> ##
> >
> >
> ##
> > ###
> > ### Running command:
> > ###
> > ###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build
> > --keep-empty-dirs --no-resave-data ERSSA
> > ###
> >
> >
> ##
> >
> >
> ##
> >
> >
> > * checking for file ‘ERSSA/DESCRIPTION’ ... OK
> > * preparing ‘ERSSA’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... ERROR
> > --- re-building ‘ERSSA.Rmd’ using rmarkdown
> > Quitting from lines 45-46 (ERSSA.Rmd)
> > Error: processing vignette 'ERSSA.Rmd' failed with diagnostics:
> > Magick: unable to open image
> >
> >
> `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png':
> > No such file or directory @ error/blob.c/OpenBlob/2701
> > --- failed re-building ‘ERSSA.Rmd’
> >
> > SUMMARY: processing the following file failed:
> >   ‘ERSSA.Rmd’
> >
> > Error: Vignette re-building failed.
> > Execution halted
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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Re: [Bioc-devel] Error unable to find image

[Leonardo Collado Torres]

Hi,

Thanks for the links!

Should we wait for the knitr fix to be available through CRAN or edit our
DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub?

Best,
Leo

On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan 
wrote:

> This seems to be a problem with a recent change to knitr
>
>   https://github.com/Bioconductor/BiocStyle/issues/71
>   https://github.com/yihui/knitr/issues/1797
>
> Please follow these issues; it looks like it is fixed in the github
> repository, but needs to be made available in CRAN for this to be fixed on
> our build systems.
>
> Martin
>
> On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" <
> bioc-devel-boun...@r-project.org on behalf of zach.s...@gmail.com> wrote:
>
> Hello,
>
> Not sure what to make of this error
>
> with building the vingette by bioconductor.
>
> The figures are all there.
>
> Did something change with knitr?
>
> Thank you.
>
>
> Zach
>
>
> ##
>
> ##
> ###
> ### Running command:
> ###
> ###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build
> --keep-empty-dirs --no-resave-data ERSSA
> ###
>
> ##
>
> ##
>
>
> * checking for file ‘ERSSA/DESCRIPTION’ ... OK
> * preparing ‘ERSSA’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘ERSSA.Rmd’ using rmarkdown
> Quitting from lines 45-46 (ERSSA.Rmd)
> Error: processing vignette 'ERSSA.Rmd' failed with diagnostics:
> Magick: unable to open image
>
> `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png':
> No such file or directory @ error/blob.c/OpenBlob/2701
> --- failed re-building ‘ERSSA.Rmd’
>
> SUMMARY: processing the following file failed:
>   ‘ERSSA.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Request R code this paper

[Leonardo Collado Torres]

Hi Joris,

I think that it's a spam email. I've gotten a similar if not the same
version directly already.

Best,
Leo

On Tue, Jan 7, 2020 at 10:48 AM Joris Meys  wrote:

> Dear,
>
> you mailed the developers mailing list of Bioconductor, i.e. the list for
> people who develop packages for the Bioconductor suite. Please mail the
> authors of the paper instead. If you know the package they used, the source
> code of each package can be found on the bioconductor website.
>
> Kind regards
> Joris
>
> --
> Joris Meys
> Statistical consultant
>
> Department of Data Analysis and Mathematical Modelling
> Ghent University
> Coupure Links 653, B-9000 Gent (Belgium)
> --
>
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
>
> 
> From: Bioc-devel  on behalf of Salwa
> El-Aty 
> Sent: Tuesday, January 7, 2020 3:49 AM
> To: Bioc-devel@r-project.org
> Subject: [Bioc-devel] Request  R code  this paper
>
> Dear Sir
> I want to help me about to send  the  R Codes of   paper which title
>   "Generalized  endpoint -inflated  binomial model" .COMPUTATION
> STATISTICS AND DATA ANALYSIS .89  , 2015
> Best Regards
> Salwa. A.Mousa
>
> Sent from my Samsung device
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] package download stats seem unavailable

[Leonardo Collado Torres]

Oops, I'm behind on my BioC Slack updates! Thanks for the reminder hehe

On Mon, Nov 11, 2019 at 8:18 PM Pages, Herve  wrote:

> Hi Leonardo,
>
> The download stats are temporarily unavailable and should be back
> tomorrow (as discussed last week on the community-bioc Slack, #general
> channel).
>
> Thanks for your patience,
>
> H.
>
> On 11/11/19 10:23, Leonardo Collado Torres wrote:
> > Hi,
> >
> > The tabular files with the Bioconductor package statistics seem broken
> > right now. For example,
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=-BdPEdtYLADOzfp_U4VQlSYBQSa2s6RI-bovMie-tqQ=
> links
> > to
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_recount-5Fstats.tab=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=vmqUUMoSwSUY-T6XNDObItzsiwQF5ypZiPDUHZJFdoA=
> > which right now redirects to a "page not found" message at
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_recount-5Fstats.tab_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=emHwGn6PRbXt8ooFXtmph_Qo6Q_yiZtns8S76AdTegk=
> > (trailing
> > slash).
> >
> > I noticed this when I wanted to add the new GenomicState pkg to my CV
> using
> > this R code
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lcolladotor_cv_blob_gh-2Dpages_en-5FCV-5Flcollado.Rnw-23L87-2DL96=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=2et8LWo_FJxTaoaapOWldNpzTq7VqFgUu5vSjH7rOzo=
> .
> > At
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_data_annotation_html_GenomicState.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=z_7YilykLuxnL4uVyhKd6r1IorqRusOv4al7hZK1cWM=
> > the
> > link to
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_data-2Dannotation_GenomicState_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=sF1DuzbvLkqkyzWFL1VhKDEKN7-fX7JJ91t9dbU4qM4=
> > (from the rank badge) returns an "Access Forbidden" result.
> >
> > Best,
> > Leo
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=imTISDYJBYS5wbRH9D8EUoa812Py7ILj1-5L6oZiJEs=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

[[alternative HTML version deleted]]

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[Bioc-devel] package download stats seem unavailable

[Leonardo Collado Torres]

Hi,

The tabular files with the Bioconductor package statistics seem broken
right now. For example,
http://bioconductor.org/packages/stats/bioc/recount/ links
to http://bioconductor.org/packages/stats/bioc/recount/recount_stats.tab
which right now redirects to a "page not found" message at
http://bioconductor.org/packages/stats/bioc/recount/recount_stats.tab/
(trailing
slash).

I noticed this when I wanted to add the new GenomicState pkg to my CV using
this R code
https://github.com/lcolladotor/cv/blob/gh-pages/en_CV_lcollado.Rnw#L87-L96.
At
http://bioconductor.org/packages/release/data/annotation/html/GenomicState.html
the
link to http://bioconductor.org/packages/stats/data-annotation/GenomicState/
(from the rank badge) returns an "Access Forbidden" result.

Best,
Leo

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Leonardo Collado Torres]

Hi,

I'm happy to report that this was never a connection issue. I was just
mislead by 
https://stackoverflow.com/questions/25487593/r-what-does-incomplete-block-on-file-mean
which suggested that the download was incomplete as well as the timing
of the connection issue with the non-bioc website. It turns out that
the installation of clusterProfiler's dependencies DO.db, GO.db and
other packages that have no Windows binary can be resolved by editing
the TMP and TEMP environment variables to a path with no spaces for a
Windows user whose username includes a space. Doing so leads to a
utils::tempdir() with no spaces, which is used to form the destination
directory with default arguments when using utils::install.packages().

I wrote more about this at
http://lcolladotor.github.io/2019/09/18/windows-user-space-issues-with-installing-r-packages/#.XYGsZJNKg0o

Thank you again for your help on this a year ago! If any of you have
other solutions, we'd love to learn about them.

Best,
Leo


On Thu, Aug 2, 2018 at 2:22 PM Leonardo Collado Torres  wrote:
>
> Thanks Hervé and no problem about the Windows binary.
>
> Richard did get DelayedArray installed today (I think using biocLite)! ^^
>
> Best,
> Leo
>
> On Thu, Aug 2, 2018 at 1:59 PM Hervé Pagès  wrote:
>>
>>
>> Hi Leonardo,
>>
>> Hope you were able to solve your connection problems.
>> Just to let you that I fixed the DelayedArray timeout on
>> Windows and the zip files are now available for this
>> platform:
>>
>>https://bioconductor.org/packages/DelayedArray
>>
>> Sorry for the inconvenience.
>>
>> Cheers,
>> H.
>>
>>
>> On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
>> > Hi,
>> >
>> > Just as a quick update. Everything worked yesterday when Richard used
>> > another PC computer from his home (another network). So it's
>> > definitely not a Bioc problem.
>> >
>> > Yet I have no idea how to troubleshoot it beyond burning it all and
>> > starting from scratch: re-installing R and everything and checking if
>> > that works. Well, or testing using a hotspot wifi connection with one
>> > of our phones and seeing if that works to bypass the wifi network from
>> > work.
>> >
>> > Best,
>> > Leo
>> >
>> > On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr.  
>> > wrote:
>> >>
>> >> are you sure his tmp directory isn't full
>> >>
>> >> --t
>> >>
>> >>
>> >> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres 
>> >>  wrote:
>> >>>
>> >>>  From Richard:
>> >>>
>> >>>> BiocManager::install("DelayedArray")
>> >>>
>> >>> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
>> >>>
>> >>> Installing package(s) 'BiocVersion', 'DelayedArray'
>> >>>
>> >>> trying URL 
>> >>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ='
>> >>>
>> >>> Content type 'application/zip' length 8649 bytes
>> >>>
>> >>> downloaded 8649 bytes
>> >>>
>> >>>
>> >>>
>> >>> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
>> >>>
>> >>>
>> >>>
>> >>> The downloaded binary packages are in
>> >>>
>> >>> C:\Users\Richard 
>> >>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
>> >>>
>> >>> installing the source package ‘DelayedArray’
>> >>>
>> >>>
>> >>>
>> >>> trying URL 
>> >>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY='
>> >>>
>> >>> Content type 'application/x-gzip' length 486139 bytes (474 KB)
>> >>>
>> >>> downloaded 474 KB
>> >>>
>> >>>
>> >>>
>> >>> Error in untar2(tarfile, files, list, exdir, restore_times) :
>> >>>
>> >>

Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

[Leonardo Collado Torres]

Hi Michael,

That was using rtracklayer 1.45.3. However I see at
https://github.com/lawremi/rtracklayer/commit/90d4209eae05ae2a4af550072c35cada662b4c89
that you made a recent change. If I use the GitHub version, it all
works =)

> result <- rtracklayer::import(sampleFile,
+ selection = regs,
+ as = 'RleList'
+ )
> result2 <- rtracklayer::import(sampleFile,
+ selection = GenomicRanges::reduce(regs),
+ as = 'RleList'
+ )
> identical(result, result2)
[1] TRUE

library('sessioninfo')
options(width = 120)
session_info()

## Same as yesterday except:
 rtracklayer1.45.32019-08-22 [1] Github
(lawremi/rtracklayer@2dac472)

Best,
Leo

On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence
 wrote:
>
> Sorry, please try 1.45.3. If that works then I'll push it over to release.
>
> On Wed, Aug 21, 2019 at 11:48 AM Leonardo Collado Torres
>  wrote:
> >
> > Dear Bioc-devel,
> >
> > In BioC 3.9 and 3.10 I've noticed some errors on recount which today I
> > finally traced. It looks like the internals of
> > rtracklayer::import.bw() changed (or mabye S4Vectors:::normarg_names)
> > in such a way that if you specify as input to rtracklayer::import()
> > the "selection" argument with a named GRanges object that has repeated
> > ranges, the function call fails. This can be avoided from a user's
> > perspective by using GenomicRanges::reduce() on the input to
> > "selection", which I guess is ultimately the best option. I now use
> > GenomicRanges::reduce() on derfinder version 1.18.4 (BioC 3.9) and
> > 1.19.4 (BioC 3.10) to solve this issue for recount. But well, I
> > thought that it would be best to share this with all of you.
> >
> > Best,
> > Leo
> >
> > Here's the actual R code for reproducing this situation:
> >
> >
> >
> > sampleFile <- c(
> > 'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.bw'
> > )
> > regs <- GenomicRanges::GRanges(
> > 'chrY',
> > IRanges::IRanges(start = c(1, 1), width = 10),
> > strand = '-'
> > )
> > names(regs) <- c(1:2)
> > result <- rtracklayer::import(sampleFile,
> > selection = regs,
> > as = 'RleList'
> > )
> > # Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
> > #   attempt to set too many names (2) on IRanges object of length 1
> >
> > # 12: stop(wmsg("attempt to set too many names (", names_len, ") ",
> > # "on ", x_class, " object of length ", x_len))
> > # 11: S4Vectors:::normarg_names(value, class(x), length(x))
> > # 10: `names<-`(`*tmp*`, value = nm)
> > # 9: `names<-`(`*tmp*`, value = nm)
> > # 8: setNames(ranges(x), value)
> > # 7: `names<-`(`*tmp*`, value = names(flatWhich))
> > # 6: `names<-`(`*tmp*`, value = names(flatWhich))
> > # 5: .local(con, format, text, ...)
> > # 4: import(FileForFormat(con), ...)
> > # 3: import(FileForFormat(con), ...)
> > # 2: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
> > # 1: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
> >
> > result <- rtracklayer::import(sampleFile,
> > selection = GenomicRanges::reduce(regs),
> > as = 'RleList'
> > )
> >
> > library('sessioninfo')
> > options(width = 120)
> > session_info()
> >
> > # ─ Session info
> > ───
> > #  setting  value
> > #  version  R version 3.6.1 (2019-07-05)
> > #  os   macOS Mojave 10.14.6
> > #  system   x86_64, darwin15.6.0
> > #  ui   X11
> > #  language (EN)
> > #  collate  en_US.UTF-8
> > #  ctypeen_US.UTF-8
> > #  tz   America/New_York
> > #  date 2019-08-21
> > #
> > # ─ Packages 
> > ───
> > #  package  * version   date   lib source
> > #  assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
> > #  backports  1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
> > #  Biobase2.45.02019-05-02 [1] Bioconductor
> > #  BiocGenerics   0.31.52019-07-03 [1] Bioconductor
> > #  BiocParallel   1.19.22019-08-07 [1] Bioconductor
> > #  Biostrings 2.53.22019-07-09 [1] Bioconductor
> > #  bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
> > #  callr  3.3.1 2019-07-18 [1] CRA

[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

[Leonardo Collado Torres]

Dear Bioc-devel,

In BioC 3.9 and 3.10 I've noticed some errors on recount which today I
finally traced. It looks like the internals of
rtracklayer::import.bw() changed (or mabye S4Vectors:::normarg_names)
in such a way that if you specify as input to rtracklayer::import()
the "selection" argument with a named GRanges object that has repeated
ranges, the function call fails. This can be avoided from a user's
perspective by using GenomicRanges::reduce() on the input to
"selection", which I guess is ultimately the best option. I now use
GenomicRanges::reduce() on derfinder version 1.18.4 (BioC 3.9) and
1.19.4 (BioC 3.10) to solve this issue for recount. But well, I
thought that it would be best to share this with all of you.

Best,
Leo

Here's the actual R code for reproducing this situation:



sampleFile <- c(
'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.bw'
)
regs <- GenomicRanges::GRanges(
'chrY',
IRanges::IRanges(start = c(1, 1), width = 10),
strand = '-'
)
names(regs) <- c(1:2)
result <- rtracklayer::import(sampleFile,
selection = regs,
as = 'RleList'
)
# Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
#   attempt to set too many names (2) on IRanges object of length 1

# 12: stop(wmsg("attempt to set too many names (", names_len, ") ",
# "on ", x_class, " object of length ", x_len))
# 11: S4Vectors:::normarg_names(value, class(x), length(x))
# 10: `names<-`(`*tmp*`, value = nm)
# 9: `names<-`(`*tmp*`, value = nm)
# 8: setNames(ranges(x), value)
# 7: `names<-`(`*tmp*`, value = names(flatWhich))
# 6: `names<-`(`*tmp*`, value = names(flatWhich))
# 5: .local(con, format, text, ...)
# 4: import(FileForFormat(con), ...)
# 3: import(FileForFormat(con), ...)
# 2: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
# 1: rtracklayer::import(sampleFile, selection = regs, as = "RleList")

result <- rtracklayer::import(sampleFile,
selection = GenomicRanges::reduce(regs),
as = 'RleList'
)

library('sessioninfo')
options(width = 120)
session_info()

# ─ Session info
───
#  setting  value
#  version  R version 3.6.1 (2019-07-05)
#  os   macOS Mojave 10.14.6
#  system   x86_64, darwin15.6.0
#  ui   X11
#  language (EN)
#  collate  en_US.UTF-8
#  ctypeen_US.UTF-8
#  tz   America/New_York
#  date 2019-08-21
#
# ─ Packages 
───
#  package  * version   date   lib source
#  assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
#  backports  1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
#  Biobase2.45.02019-05-02 [1] Bioconductor
#  BiocGenerics   0.31.52019-07-03 [1] Bioconductor
#  BiocParallel   1.19.22019-08-07 [1] Bioconductor
#  Biostrings 2.53.22019-07-09 [1] Bioconductor
#  bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
#  callr  3.3.1 2019-07-18 [1] CRAN (R 3.6.0)
#  cli1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
#  colorout * 1.2-1 2019-07-27 [1] Github
(jalvesaq/colorout@7ea9440)
#  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
#  DelayedArray   0.11.42019-07-03 [1] Bioconductor
#  desc   1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
#  devtools * 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
#  digest 0.6.202019-07-04 [1] CRAN (R 3.6.0)
#  fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
#  GenomeInfoDb   1.21.12019-05-16 [1] Bioconductor
#  GenomeInfoDbData   1.2.1 2019-07-27 [1] Bioconductor
#  GenomicAlignments  1.21.42019-06-28 [1] Bioconductor
#  GenomicRanges  1.37.14   2019-06-24 [1] Bioconductor
#  glue   1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
#  IRanges2.19.10   2019-06-11 [1] Bioconductor
#  lattice0.20-38   2018-11-04 [1] CRAN (R 3.6.1)
#  magrittr   1.5   2014-11-22 [1] CRAN (R 3.6.0)
#  Matrix 1.2-172019-03-22 [1] CRAN (R 3.6.1)
#  matrixStats0.54.02018-07-23 [1] CRAN (R 3.6.0)
#  memoise1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
#  pkgbuild   1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
#  pkgload1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
#  prettyunits1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
#  processx   3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
#  ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
#  R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
#  Rcpp   1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
#  RCurl  1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
#  remotes2.1.0 2019-06-24 [1] CRAN (R 

Re: [Bioc-devel] Canceled event: Biocondutor Developers Forum @ Thu Aug 15, 2019 12pm - 1pm (EDT) (bioc-devel@r-project.org)

[Leonardo Collado Torres]

Hi everyone,

I think this caused a bit of confusion. My understanding was that Sean
created a google calendar event and cc'ed the bioc-dev mailing list.
In any case, from what I can see at the BioC slack in the #general
channel, the forum is still scheduled for tomorrow Thursday August
15th.


Aaron Lun 1:38 AM
So. Uh. This dev forum thing. Is it still on, or what?
Today at 8:21 AM
Martin Morgan 6:17 AM
yep, Thursday 12 noon Eastern details at
https://stat.ethz.ch/pipermail/bioc-devel/2019-August/015359.html
there's also a #developers-forum

Best,
Leo

On Thu, Aug 8, 2019 at 9:50 AM  wrote:
>
> This event has been canceled.
>
> Title: [Bioc-devel] Biocondutor Developers Forum
> Dear all,
>
> I am excited to announce a new initiative within the Bioconductor project -
> the Bioconductor Developers' Forum.  This monthly teleconference is
> intended as a platform for Bioconductor developers to describe existing
> software infrastructure to other members of the BioC community, to present
> plans for future developments, and discuss changes that may impact other
> developers or software tools within the Bioconductor.
>
> The intended audience is anyone interested in software development and
> infrastructure, whether you're a member of the BioC core team with
> responsibility for multiple packages, or you're just getting started with
> creating a Bioconductor package.
>
> Our first meeting will take place on Thursday 15th August at 09:00 PDT/
> 12:00 EDT / 18:00 CEST using BlueJeans and can be joined via:
>
> https://bluejeans.com/136043474?src=join_info (Meeting ID: 136 043 474)
>
> More details on the...
> When: Thu Aug 15, 2019 12pm – 1pm Eastern Time - New York
> Calendar: bioc-devel@r-project.org
> Who:
>  * seand...@gmail.com - organizer
>  * peter.hic...@gmail.com
>  * grimbo...@gmail.com
>  * bioc-devel@r-project.org
>
>
> Invitation from Google Calendar: https://www.google.com/calendar/
>
> You are receiving this courtesy email at the account
> bioc-devel@r-project.org because you are an attendee of this event.
>
> To stop receiving future updates for this event, decline this event.
> Alternatively you can sign up for a Google account at
> https://www.google.com/calendar/ and control your notification settings for
> your entire calendar.
>
> Forwarding this invitation could allow any recipient to send a response to
> the organizer and be added to the guest list, or invite others regardless
> of their own invitation status, or to modify your RSVP. Learn more at
> https://support.google.com/calendar/answer/37135#forwarding
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Event addition request: CDSB Workshop 2019 in Cuernavaca, Mexico

[Leonardo Collado Torres]

Awesome, thanks Lori!

Best,
Leo

On Tue, Jun 11, 2019 at 8:43 AM Shepherd, Lori
 wrote:
>
> I believe it now should be added to the event list.  It could take up to an 
> hour to appear officially on the website.  Sometimes there is a delay to 
> appearing on the website,  if its not up by tomorrow please let us know and 
> we will look into any issues.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________
> From: Bioc-devel  on behalf of Leonardo 
> Collado Torres 
> Sent: Monday, June 10, 2019 2:50:14 PM
> To: Bioc-devel
> Subject: [Bioc-devel] Event addition request: CDSB Workshop 2019 in 
> Cuernavaca, Mexico
>
> Hi,
>
> Would it be possible to add a link like "[CDSB Workshop
> 2019](https://comunidadbioinfo.github.io/post/building-tidy-tools-cdsb-runconf-2019/#.XP6kUNNKi52)
> July 29-August 2, 2019, Cuernavaca, Mexico" at
> http://bioconductor.org/help/events/? It's a one week workshop where
> Alejandro Reyes, me and others will teach how to build R packages
> (following Charlotte and Hadley's "Building Tidy Tools" workshop) and
> then spend 2 days practicing how to do so (following rOpenSci
> runconf18's style). It's part of the EBM2019 (Encuentro de
> Bioinformática en México http://congresos.nnb.unam.mx/TIB2019/) that
> also includes a one week R/RStudio introduction course. And well, it's
> basically our 2019 version of what we did last year with Martin Morgan
> and others in order to help more Latino Americans contribute to
> Bioconductor and other R communities. Check
> https://comunidadbioinfo.github.io/post/path-from-cdsbmexico-2018-to-bioc2019/#.XP6kV9NKi50
> for the story on how we helped 3 new members attend BioC2019.
>
> If you know anyone interested, here's also the link in Spanish for
> 2019 workshop: 
> https://comunidadbioinfo.github.io/es/post/building-tidy-tools-cdsb-runconf-2019/#.XP6lwtNKi50
>
> Thank you!
> Leo
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.

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[Bioc-devel] Event addition request: CDSB Workshop 2019 in Cuernavaca, Mexico

[Leonardo Collado Torres]

Hi,

Would it be possible to add a link like "[CDSB Workshop
2019](https://comunidadbioinfo.github.io/post/building-tidy-tools-cdsb-runconf-2019/#.XP6kUNNKi52)
July 29-August 2, 2019, Cuernavaca, Mexico" at
http://bioconductor.org/help/events/? It's a one week workshop where
Alejandro Reyes, me and others will teach how to build R packages
(following Charlotte and Hadley's "Building Tidy Tools" workshop) and
then spend 2 days practicing how to do so (following rOpenSci
runconf18's style). It's part of the EBM2019 (Encuentro de
Bioinformática en México http://congresos.nnb.unam.mx/TIB2019/) that
also includes a one week R/RStudio introduction course. And well, it's
basically our 2019 version of what we did last year with Martin Morgan
and others in order to help more Latino Americans contribute to
Bioconductor and other R communities. Check
https://comunidadbioinfo.github.io/post/path-from-cdsbmexico-2018-to-bioc2019/#.XP6kV9NKi50
for the story on how we helped 3 new members attend BioC2019.

If you know anyone interested, here's also the link in Spanish for
2019 workshop: 
https://comunidadbioinfo.github.io/es/post/building-tidy-tools-cdsb-runconf-2019/#.XP6lwtNKi50

Thank you!
Leo

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Re: [Bioc-devel] Procedure for changing email

[Leonardo Collado Torres]

Hi Nitesh,

I believe that I completed my email change everywhere where I needed
to including https://git.bioconductor.org/BiocCredentials/profile/
(which I didn't remember about, thanks!).

Best,
Leo

On Mon, May 20, 2019 at 9:15 PM Turaga, Nitesh
 wrote:
>
> Hi Leo,
>
> If your old email is registered to the BiocCredentials app, then you'd have 
> to change that too.
>
> If you reply with that email, a Bioc admin can change it for you (me).
>
> Best
>
> Nitesh
>
> Get Outlook for Android
>
> ____
> From: Bioc-devel  on behalf of Leonardo 
> Collado Torres 
> Sent: Monday, May 20, 2019 3:50:01 PM
> To: Bioc-devel
> Subject: [Bioc-devel] Procedure for changing email
>
> Hi,
>
> I couldn't find at http://bioconductor.org/help/support/ or at the
> support website ("change email" search) the steps for changing an
> email.
>
> My understanding is that this requires changing the email in 4 locations:
>
> * bioc-devel mailing list through
> https://stat.ethz.ch/mailman/options/bioc-devel
> * The BioC user support website through "edit my profile" (in my case
> https://support.bioconductor.org/u/edit/6526/)
> * a request to the bioc-devel for updating the maintainer email for
> the related packages (for git?)
> * updating the DESCRIPTION file in the release and devel branches of
> all the packages the email is listed in
>
> Am I missing another location where the email needs to change? What is
> the ideal order?
>
> Best,
> Leo
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.

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[Bioc-devel] Procedure for changing email

[Leonardo Collado Torres]

Hi,

I couldn't find at http://bioconductor.org/help/support/ or at the
support website ("change email" search) the steps for changing an
email.

My understanding is that this requires changing the email in 4 locations:

* bioc-devel mailing list through
https://stat.ethz.ch/mailman/options/bioc-devel
* The BioC user support website through "edit my profile" (in my case
https://support.bioconductor.org/u/edit/6526/)
* a request to the bioc-devel for updating the maintainer email for
the related packages (for git?)
* updating the DESCRIPTION file in the release and devel branches of
all the packages the email is listed in

Am I missing another location where the email needs to change? What is
the ideal order?

Best,
Leo

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Re: [Bioc-devel] Packages with broken unit tests because of sample() change in R 3.6

[Leonardo Collado Torres]

Thanks Hervé,

I also found this tweet by John Muschelli useful for this situation
https://twitter.com/StrictlyStat/status/1103303028751372289 where he
suggests using suppressWarnings(RNGversion("3.5.0"))

That's what I did for example in
https://github.com/leekgroup/derfinderHelper/commit/c2c756d6e1f6c3da219073a6c36c2b475453ecf1
to resolve the issue with derfinderHelper.

Best,
Leo

On Mon, Apr 8, 2019 at 6:40 PM Pages, Herve  wrote:
>
> Dear developers,
>
> As reported on this list in March 
> (https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html) the 
> sample() function has changed in recent R-devel. This change breaks the 19 
> following Bioconductor software packages:
>
>   - cicero
>   - clipper
>   - clusterExperiment
>   - CMA
>   - CNVPanelizer
>   - derfinder
>   - derfinderHelper
>   - flowQB
>   - mAPKLA
>   - MCbiclust
>   - Melissa
>   - metaseqR
>   - nucleoSim
>   - onlineFDR
>   - PathNet
>   - phyloseq
>   - SPONGE
>   - treeio
>   - trena
>
>
> For all these packages (except for the CMA package), the change to sample() 
> breaks the unit tests where sample() is used to generate random data as input 
> to the test. Since sample() generates different random numbers in R 3.6 
> (compared to R 3.5, with the seed set to the same value), the input to the 
> test now is different and so is its output, so comparison to the old expected 
> result now fails. The fix is to simply modify the expected result to match 
> the new output.
>
> If you maintain one of the above package, please fix your package as soon as 
> possible.
>
> Keep in mind that all Bioconductor packages will need to pass 'R CMD build' 
> and 'R CMD check' with no error in order to be included in the next 
> Bioconductor release, scheduled for Tuesday April 30. Note that Bioconductor 
> 3.9 will be based on R 3.6 (scheduled to be released on Friday April 26) so 
> please make sure to use a recent version of R devel when testing/fixing your 
> package.
>
> See our release schedule:
>
>   https://bioconductor.org/developers/release-schedule/
>
> and this recent announcement on this list:
>
>   https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014832.html
>
> Thank you for your ongoing contribution to Bioconductor.
>
> Cheers,
>
> H.
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] GenomicFeatures export request

[Leonardo Collado Torres]

Awesome, thanks Hervé!

Best,
Leo

On Wed, Dec 5, 2018 at 1:55 PM Pages, Herve  wrote:

> Hi Leo,
>
> This is done in GenomicFeatures 1.35.4:
>
>
> https://github.com/Bioconductor/GenomicFeatures/commit/0b596c18b69f55d097aff0c6cdbbfc0b2993c4aa
>
> Cheers,
>
> H.
>
>
> On 11/15/18 09:25, Leonardo Collado Torres wrote:
> > Hi Hervé,
> >
> > Looking into the details of GenomicFeatures::exonicParts() I see that
> > this function runs GenomicFeatures:::.tidy_exons(). Would it be
> > possible to export this function? Looks like it'll be useful for some
> > work we are doing.
> >
> > We can start using it without the function being exported, and well,
> > if you prefer not to export it we could still use it in other packages
> > (though a NOTE will show up in R CMD check).
> >
> > I don't think that we'll use GenomicFeatures:::.tidy_transcripts()
> > directly although GenomicFeatures:::.tidy_exons() runs it. But well,
> > maybe other users might be interested in your tidy set of functions.
> >
> > Best,
> > Leo
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>

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[Bioc-devel] GenomicFeatures export request

[Leonardo Collado Torres]

Hi Hervé,

Looking into the details of GenomicFeatures::exonicParts() I see that
this function runs GenomicFeatures:::.tidy_exons(). Would it be
possible to export this function? Looks like it'll be useful for some
work we are doing.

We can start using it without the function being exported, and well,
if you prefer not to export it we could still use it in other packages
(though a NOTE will show up in R CMD check).

I don't think that we'll use GenomicFeatures:::.tidy_transcripts()
directly although GenomicFeatures:::.tidy_exons() runs it. But well,
maybe other users might be interested in your tidy set of functions.

Best,
Leo

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Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

[Leonardo Collado Torres]

Thank you for the info Martin and Michael!

In the particular situation with recount and the xts warning,
re-installing data.table 1.11.8 worked with xts 0.11.2. Details are
further below.

Best,
Leo

On Mon, Nov 5, 2018 at 6:49 PM Michael Lawrence
 wrote:
>
> For the general problem of understanding your package dependency structure, 
> see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.


Thanks for the link!

>
>
> On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan  wrote:
>>
>>
>>
>> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" 
>>  wrote:
>>
>> Hi bioc-devel,
>>
>> recount is getting a warning on Bioc 3.9 (devel) on macOS:
>>
>> * checking whether package ‘recount’ can be installed ... WARNING
>> Found the following significant warnings:
>>   Warning: S3 method ‘xts::as.xts.data.table’ was declared in
>> NAMESPACE but not found
>>
>> I'm not sure how to trace this since recount doesn't depend on xts. At
>> least not directly. What is the best way to find which of the recount
>> dependencies is triggering this NAMESPACE warning? While it's a
>> warning in this case, it seems to break the installation of the GitHub
>> package LieberInstitute/recount.bwtool as shown below.
>>
>> Can you reproduce this warning when you load recount in a new session? If 
>> so, you can
>>
>>   options(warn = 2) # make them errors
>>   trace(registerS3methods, tracer = quote(print(package)))
>>   library(recount)


Thanks, I didn't know about trace(regiserS3methods, tracer =
quote(print(package))) ! And yes, I can reproduce the problem with
this code.

>>
>>
>> which will print out each package as it is loaded, the last being printed is 
>> the culprit.
>>
>> This failed a problem for me, but on the builder I see
>>
>> Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
>> [1] "data.table"
>> Error: package or namespace load failed for ‘recount’:
>>  (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in 
>> NAMESPACE but not found
>>
>> The builder has
>>
>> > packageVersion("xts")
>> [1] ‘0.11.1’
>>
>> whereas I have 0.11.2. The reason is because my R installs xts from source 
>> where the most recent version is 0.11.2, whereas the builder plays like most 
>> mac users and installs built binaries. The last mac binary available is 
>> 0.11.1, as summarized here:
>>
>>   https://cran.r-project.org/web/packages/xts/index.html
>>
>> where the Published date is 2018-11-05 (today!) and where the binaries are 
>> 0.11.1 but source is 0.11.2.



Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
[1] "data.table"
Error: package or namespace load failed for ‘recount’:
 (converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
>
> packageVersion('xts')
[1] ‘0.11.2’
>
> sessionInfo()
R Under development (unstable) (2018-11-02 r75540)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] SummarizedExperiment_1.13.0 DelayedArray_0.9.0
 [3] BiocParallel_1.17.0 matrixStats_0.54.0
 [5] Biobase_2.43.0  GenomicRanges_1.35.0
 [7] GenomeInfoDb_1.19.0 IRanges_2.17.0
 [9] S4Vectors_0.21.0BiocGenerics_0.29.1
[11] colorout_1.2-0

loaded via a namespace (and not attached):
 [1] bitops_1.0-6 bit64_0.9-7  RColorBrewer_1.1-2
 [4] progress_1.2.0   httr_1.3.1   GenomicFiles_1.19.0
 [7] tools_3.6.0  backports_1.1.2  R6_2.3.0
[10] rpart_4.1-13 DBI_1.0.0lazyeval_0.2.1
[13] colorspace_1.3-2 nnet_7.3-12  tidyselect_0.2.5
[16] gridExtra_2.3prettyunits_1.0.2bit_1.1-14
[19] compiler_3.6.0   htmlTable_1.12   xml2_1.2.0
[22] rtracklayer_1.43.0   scales_1.0.0 checkmate_1.8.5
[25] readr_1.1.1  stringr_1.3.1digest_0.6.18
[28] Rsamtools_1.35.0 foreign_0.8-71   GEOquery_2.51.0
[31] XVector_0.23.0   base64enc_0.1-3  pkgconfig_2.0.2
[34] htmltools_0.3.6  limma_3.39.1 BSgenome_1.5

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

[Leonardo Collado Torres]

Thanks for fixing this Nitesh and Sam!

I wrote that R check and forgot that it depended on the Gencode url. I
had to fix this too for recount
https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e.

Best,
Leo


On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh
 wrote:
>
> Hi Sam,
>
> I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the 
> commit history for RELEASE_3_8 though, (which I fixed in 
> git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in 
> rafalab/bumphunter.
>
> The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
>
> 7437f04 Apply interval bugfix to sanitized master branch
> a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8 
> branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> The commit showing "bump x.y.z versions to odd y after creation of 
> RELEASE_3_8 branch”  should not be in the RELEASE_3_8 branch. The version 
> number in the RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z 
> version numbering scheme.
>
> After fixing your RELEASE_3_8 branch now looks like this,
>
> 96fd715 Bump version after cherry-picking bug fix,
> ac34111 Apply interval bugfix to sanitized master branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should 
> now build on RELEASE_3_8 if the fix works.
>
> NOTE: After a push is made it can take up to 48 hours for it to
> appear on the build report and landing pages - i.e. we do one pull,
> build, check, propagate in 24 hours - so if your commit was after the pull
> for the day it wont be until the following day
>
>
> Best,
>
> Nitesh
>
>
> > On Nov 5, 2018, at 2:56 PM, Samuela Pollack  
> > wrote:
> >
> > Hi Nitesh,
> >
> > I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch, 
> > and request synchronization with Bioconductor RELEASE_3_8. We need this, 
> > because bumphunter is not building on RELEASE_3_8, due to an obsolete URL 
> > in one of the tests.
> >
> > thanks,
> >
> > - Sam
> >
> >
> > On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
> >> External Email - Use Caution
> >>
> >> Hi Sam,
> >>
> >> I have updated your “master” branch on git.bioconductor.com to reflect 
> >> what you have on GitHub, at https://github.com/rafalab/bumphunter.  You 
> >> will not get the duplicate commit error when you push to the master branch 
> >> anymore.
> >>
> >> However, RELEASE_3_8 still has duplicate commits in the history. You could 
> >> follow the same procedure as you did for the master branch, and 
> >> de-duplicate the commit history for RELEASE_3_8. You should invest time in 
> >> this only if you think there will be any changes made to the release 
> >> branch. If not, then this is not an issue. If you do choose to follow 
> >> through with RELEASE_3_8 as well, please reply to this thread when you 
> >> have made the de-duplication changes and added the branch to your GitHub 
> >> repository.
> >>
> >> Best regards,
> >>
> >> Nitesh
> >>
> >>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack  
> >>> wrote:
> >>>
> >>> Dear Bioconductor,
> >>>
> >>> I believe I have removed all duplicate commits from the bumphunter 
> >>> package. The main branch in rafalab/bumphunter incorporates the new 
> >>> commit history. It passes 'library(devtools); build("."); install(); 
> >>> check("."); BiocCheck(".")'
> >>>
> >>> I am contacting you in accordance with item 6 of the instructions at this 
> >>> URL: 
> >>> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
> >>>
> >>> - Sam
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >> This email message may contain legally privileged and/or confidential 
> >> information.  If you are not the intended recipient(s), or the employee or 
> >> agent responsible for the delivery of this message to the intended 
> >> recipient(s), you are hereby notified that any disclosure, copying, 
> >> distribution, or use of this email message is prohibited.  If you have 
> >> received this message in error, please notify the sender immediately by 
> >> e-mail and delete this email message from your computer. Thank you.
> >
>
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
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[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

[Leonardo Collado Torres]

Hi bioc-devel,

recount is getting a warning on Bioc 3.9 (devel) on macOS:

* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
  Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found

I'm not sure how to trace this since recount doesn't depend on xts. At
least not directly. What is the best way to find which of the recount
dependencies is triggering this NAMESPACE warning? While it's a
warning in this case, it seems to break the installation of the GitHub
package LieberInstitute/recount.bwtool as shown below.

Anyhow, I might just wait a while as was recommended in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
Though it's worrisome if a package can't depend on recount right now
on R 3.6 / Bioc 3.9.

Thanks,
Leo

Main links:

* 
https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
* https://github.com/leekgroup/recount
* https://github.com/LieberInstitute/recount.bwtool

Full info:

> library('devtools')
> install_github('LieberInstitute/recount.bwtool')
Downloading GitHub repo LieberInstitute/recount.bwtool@master
Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
XVector, zlibbioc
✔  checking for file
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
(350ms)
─  preparing ‘recount.bwtool’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘recount.bwtool_0.99.29.tar.gz’

Loading required package: colorout
* installing *source* package ‘recount.bwtool’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘recount’:
 (converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
Error : package ‘recount’ could not be loaded
ERROR: lazy loading failed for package ‘recount.bwtool’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
Error in i.p(...) :
  (converted from warning) installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status
> traceback()
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
17: .signalSimpleWarning("installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status",
base::quote(i.p(...)))
16: warning(gettextf("installation of package %s had non-zero exit status",
sQuote(update[i, 1L])), domain = NA)
15: i.p(...)
14: force(code)
13: force(code)
12: with_envvar(c(R_PROFILE_USER = temp_rprofile), {
force(code)
})
11: with_rprofile_user("options(warn = 2)", i.p(...))
10: force(code)
9: with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
   i.p(...)))
8: force(code)
7: with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib),
   if (should_error_for_warnings()) {
   with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
   i.p(...)))
   } else {
   i.p(...)
   })
6: safe_install_packages(pkgdir, repos = NULL, quiet = quiet, type = "source",
   ...)
5: install(source, dependencies = dependencies, upgrade = upgrade,
   force = force, quiet = quiet, build = build, build_opts = build_opts,
   repos = repos, type = type, ...)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
2: install_remotes(remotes, auth_token = auth_token, host = host,
   dependencies = dependencies, upgrade = upgrade, force = force,
   quiet = quiet, build = build, build_opts = build_opts, repos = repos,
   type = type, ...)
1: install_github("LieberInstitute/recount.bwtool")

> library('recount')
Warning message:
S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found

> options(width = 120)
> sessioninfo::session_info()
─ Session info 
───
 setting  value
 version  R Under development (unstable) (2018-11-02 r75540)
 os   macOS Mojave 

Re: [Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

[Leonardo Collado Torres]

Thanks for the info Kasper!

On Sun, Nov 4, 2018 at 11:28 AM Kasper Daniel Hansen
 wrote:
>
> You seem to install the Beta version of the Command Line tools.  That's not 
> right.  Look at the top of
>   apple.com/developer/downloads
> (First try with xcode-select --install on the command line, which I could not 
> get to work).

I also tried that command and it didn't work for me either.

>
> Following installation of these tools you need to run the following command 
> which can be found in the R-admin manual (devel version of R, not the rebased 
> version)
>   https://cran.r-project.org/doc/manuals/r-devel/R-admin.html

Ahh, I didn't know about this section of the manual. Thanks!

> in section C.3:
>
> sudo installer -pkg \
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>  \
> -target /
>
> On Fri, Nov 2, 2018 at 4:05 PM Leonardo Collado Torres  
> wrote:
>>
>> Hi,
>>
>> I was about to send the email below, but eventually I got it to work.
>> I'm sharing it anyway since others might run into similar issues.
>>
>> Basically, I needed the latest macOS command line tools installed, but
>> getting them installed was tricky. I installed Xcode 10.1 (10B61) from
>> the Mac App Store, then installed a version of the command line tools
>> via 
>> https://download.developer.apple.com/Developer_Tools/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2.dmg,
>> rebooted, then under "settings", "software update" detected that there
>> was a newer version. Finally, I was then able to install the backports
>> R package.
>>
>> Best,
>> Leo
>>
>>
>>
>> ## Successful install:
>>
>> > install.packages('backports')
>> Warning: unable to access index for repository
>> https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
>>   cannot open URL
>> 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
>> Package which is only available in source form, and may need
>>   compilation of C/C++/Fortran: ‘backports’
>> Do you want to attempt to install these from sources? (Yes/no/cancel) y
>> installing the source package ‘backports’
>>
>> trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.2.tar.gz'
>> Content type 'application/x-gzip' length 10900 bytes (10 KB)
>> ==
>> downloaded 10 KB
>>
>> * installing *source* package ‘backports’ ...
>> ** package ‘backports’ successfully unpacked and MD5 sums checked
>> ** libs
>> /usr/local/clang4/bin/clang
>> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>> -I/usr/local/include   -fPIC  -Wall -g -O2  -c dotsElt.c -o dotsElt.o
>> /usr/local/clang4/bin/clang
>> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>> -I/usr/local/include   -fPIC  -Wall -g -O2  -c dotsLength.c -o
>> dotsLength.o
>> /usr/local/clang4/bin/clang
>> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
>> /usr/local/clang4/bin/clang++ -dynamiclib
>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup
>> -single_module -multiply_defined suppress
>> -L/Library/Frameworks/R.framework/Resources/lib
>> -L/usr/local/clang4/lib -o backports.so dotsElt.o dotsLength.o init.o
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>> ld: warning: text-based stub file
>> /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
>> and library file
>> /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation
>> are out of sync. Falling back to library file for linking.
>> installing to 
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/backports/libs
>> ** R
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> Loading required package: colorout
>> devtools::install_github("jalvesaq/colorout")
>> Warning message:
>> In library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE,  :
>>   there is no package called ‘colorout’
>> * DONE (backports)
>>
>> The downloaded source packages are in
>> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/RtmpBZUipc/downloaded_packages’
>> >
>> > sessionInfo()
>>

[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

[Leonardo Collado Torres]

Hi,

I was about to send the email below, but eventually I got it to work.
I'm sharing it anyway since others might run into similar issues.

Basically, I needed the latest macOS command line tools installed, but
getting them installed was tricky. I installed Xcode 10.1 (10B61) from
the Mac App Store, then installed a version of the command line tools
via 
https://download.developer.apple.com/Developer_Tools/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2.dmg,
rebooted, then under "settings", "software update" detected that there
was a newer version. Finally, I was then able to install the backports
R package.

Best,
Leo



## Successful install:

> install.packages('backports')
Warning: unable to access index for repository
https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘backports’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source package ‘backports’

trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.2.tar.gz'
Content type 'application/x-gzip' length 10900 bytes (10 KB)
==
downloaded 10 KB

* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** libs
/usr/local/clang4/bin/clang
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/include   -fPIC  -Wall -g -O2  -c dotsElt.c -o dotsElt.o
/usr/local/clang4/bin/clang
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/include   -fPIC  -Wall -g -O2  -c dotsLength.c -o
dotsLength.o
/usr/local/clang4/bin/clang
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
/usr/local/clang4/bin/clang++ -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup
-single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib
-L/usr/local/clang4/lib -o backports.so dotsElt.o dotsLength.o init.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
ld: warning: text-based stub file
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
and library file
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation
are out of sync. Falling back to library file for linking.
installing to 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Loading required package: colorout
devtools::install_github("jalvesaq/colorout")
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE,  :
  there is no package called ‘colorout’
* DONE (backports)

The downloaded source packages are in
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/RtmpBZUipc/downloaded_packages’
>
> sessionInfo()
R Under development (unstable) (2018-04-05 r74542)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0tcltk_3.6.0







## Older email:




Hi,

With Bioconductor 3.9 now being live, I got a few emails about some of
my packages which I wanted to look into. For that I tried installing R
3.6 with all my current R 3.5 packages. I quickly ran into problems
trying to install devtools. Basically, the backports package is not
available as a binary and the compilation from source fails because it
can't find an stdlib.h file. I also recently updated my Mac with the
new OS as well as the latest Xcode (which in theory now comes with the
command line tools that should include that stdlib.h file). I also
installed the latest command line tools but still ran into the same
issue.

Has anyone else seen this issue and resolved it? If so, what step and I missing?

Thanks,
Leo


> install.packages('backports')
Warning: unable to access index for repository
https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘backports’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source 

Re: [Bioc-devel] Roxygen documentation under windows

[Leonardo Collado Torres]

Hi,

Adding the -class part will help for most. To get the correct name,
check the top left part of the help page for the function you want to
link to. For example, if you type

library(GenomicRanges)
?GRanges

you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac
right now).

Here are some examples that I fixed on my packages
https://github.com/lcolladotor/derfinder/commit/2dee40434b8916a2e8acc717e3300c07ad5236b2

Best,
Leo

On Mon, Oct 8, 2018 at 9:00 AM Shepherd, Lori
 wrote:
>
> I think there is a reference here
>
> https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi
>
>
> Where the actual name of the man file that has BiocParallelParam is  
> BiocParallelParm-class and BiocParallelParam is an alias.
>
>
> I believe if you change the link to be
>
> \code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}}  It 
> should remedy the issue.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Christian 
> Mertes 
> Sent: Sunday, October 7, 2018 9:01:35 PM
> To: bioc-devel
> Subject: [Bioc-devel] Roxygen documentation under windows
>
> Hey all,
>
> I have a question. My package builds perfectly on Linux and MacOS, but fails 
> to link my documentation correctly on Windows, which results in a warning.
>
> The exact error which I get is:
> Rd warning: 
> C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpei0FPy/R.INSTALL215c42273ec6/OUTRIDER/man/OUTRIDER.Rd:22:
>  file link 'BiocParallelParam' in package 'BiocParallel' does not exist and 
> so has been treated as a topic
> The line in my code which generates this is:
>
> #' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
>
> The error can also be found here:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html
>  
> 
>
> For me it looks odd since it compiles without any error on Linux and MacOS 
> but not on Windows. So I�m not sure if its a bug on Windows or the way I�m 
> linking it in my Roxygen2 documentation.
>
> Any help is appreciated.
>
> Thanks,
>
> Christian
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>

___
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Re: [Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

[Leonardo Collado Torres]

Hi bioc-devel,

Thanks to Nitesh Turaga we were able to get derfinderData back in
sync. Basically:

* We discarded the previous GitHub repo (deleted forever)
* Re-synced via
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
* The real issue was a bug in the bump version script back in 2014
that bumped the package from 0.99.3 to 0.101.0 instead of 1.1.0
https://github.com/leekgroup/derfinderData/commit/5ea1d9580a4086ecea44cef696679a7e248ff2ab
* Nitesh fixed this manually:
https://github.com/leekgroup/derfinderData/commit/a9ba347501d92ffb2039d01d53159ebe69924b99
* See all new commits: https://github.com/leekgroup/derfinderData/commits/master

Thanks for the input Marcel!

Best,
Leo

On Tue, Sep 25, 2018 at 10:42 PM Ramos Perez, Marcel
 wrote:
>
>
> Hi Leonardo,
>
> Keep in mind that GitHub and the Bioconductor git server are two
> different animals.
>
> You should be pushing your changes to the git server as you would with
> software
> packages ( `g...@git.bioconductor.org:packages/derfinderData` ).
>
> My guess is that the hook is looking at the version already in the git
> server and
> comparing that to the committed changes (but I could be wrong).
>
> Nitesh can elaborate a bit more on this.
>
> We will look into it on our end.
>
> Regards,
>
> Marcel
>
>
>
>
> On 09/24/2018 10:54 AM, Leonardo Collado Torres wrote:
> > Hi,
> >
> > Marcel Ramos told me a few months ago (July 24, 2018) that experiment
> > data packages are now controlled the same way as software packages via
> > GitHub. Today I finally tried synching the repos following these
> > instructions 
> > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> > I had to use the "git merge --allow-unrelated-histories
> > upstream/master" step and resolve 3 small conflicts. It's almost all
> > working well, the step I'm stuck at is:
> >
> > $ git push upstream master
> > Counting objects: 45, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (38/38), done.
> > Writing objects: 100% (45/45), 5.98 KiB | 1.50 MiB/s, done.
> > Total 45 (delta 25), reused 5 (delta 4)
> > remote: Error: Illegal version bump from '0.115.0' to '0.115.1'. Check
> > remote: http://bioconductor.org/developers/how-to/version-numbering/
> > remote: for details
> > To git.bioconductor.org:packages/derfinderData.git
> >  ! [remote rejected] master -> master (pre-receive hook declined)
> > error: failed to push some refs to
> > 'g...@git.bioconductor.org:packages/derfinderData.git'
> >
> > My guess is that the hook is looking at
> > https://github.com/leekgroup/derfinderData/commit/90971f8c8f6b4116d939309942a781bc5f55d9d8
> > and thinks that I'm trying to bump from 0.103.1 to 0.115.1 while in
> > reality the version at
> > http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> > is 0.115.0 (updated in
> > https://github.com/leekgroup/derfinderData/commit/dbf71bbd4418be5a80a6060df8f5f16379a01cb3).
> >
> > Is there something I can do to make this work?
> >
> > GitHub: https://github.com/leekgroup/derfinderData
> > Bioc-devel: 
> > http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> >
> > PS I guess that I don't need this file anymore:
> > https://github.com/leekgroup/derfinderData/blob/master/external_data_store.txt
> > nor the currently untracked svn files:
> >
> > $ git status
> > On branch master
> > Your branch is up to date with 'origin/master'.
> >
> > Untracked files:
> >   (use "git add ..." to include in what will be committed)
> >
> > data/.svn/
> > inst/extdata/.svn/
> >
> > Best,
> > Leo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

[Leonardo Collado Torres]

Hi,

Marcel Ramos told me a few months ago (July 24, 2018) that experiment
data packages are now controlled the same way as software packages via
GitHub. Today I finally tried synching the repos following these
instructions 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.
I had to use the "git merge --allow-unrelated-histories
upstream/master" step and resolve 3 small conflicts. It's almost all
working well, the step I'm stuck at is:

$ git push upstream master
Counting objects: 45, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (38/38), done.
Writing objects: 100% (45/45), 5.98 KiB | 1.50 MiB/s, done.
Total 45 (delta 25), reused 5 (delta 4)
remote: Error: Illegal version bump from '0.115.0' to '0.115.1'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/derfinderData.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/derfinderData.git'

My guess is that the hook is looking at
https://github.com/leekgroup/derfinderData/commit/90971f8c8f6b4116d939309942a781bc5f55d9d8
and thinks that I'm trying to bump from 0.103.1 to 0.115.1 while in
reality the version at
http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
is 0.115.0 (updated in
https://github.com/leekgroup/derfinderData/commit/dbf71bbd4418be5a80a6060df8f5f16379a01cb3).

Is there something I can do to make this work?

GitHub: https://github.com/leekgroup/derfinderData
Bioc-devel: 
http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html

PS I guess that I don't need this file anymore:
https://github.com/leekgroup/derfinderData/blob/master/external_data_store.txt
nor the currently untracked svn files:

$ git status
On branch master
Your branch is up to date with 'origin/master'.

Untracked files:
  (use "git add ..." to include in what will be committed)

data/.svn/
inst/extdata/.svn/

Best,
Leo

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Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

[Leonardo Collado Torres]

Hi Nitesh,

After looking more closely, I went with option 1 that you clearly
outlined below. The cherry picked version of the history is now the
origin/master one at
https://github.com/jtleek/sva-devel/commits/master. From
http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
my understanding is that now you have to force the Bioconductor git
history (upstream/master with the default setup) to match the one from
the sva-devel GitHub repo.

The only complicated commit was
https://github.com/jtleek/sva-devel/commit/e6b80f62d494f77465650cf3d624feaf8913e837
where I had to use the "theirs" strategy for many files.

At the end I added this commit
https://github.com/jtleek/sva-devel/commit/05cfab55c893b428061ab703f3abd235889a
that bumps the version of the package to 3.29.1 on bioc-devel to
propagate Claire's recent changes.

Best,
Leo

PS I tried the git push -f upstream/master out of curiousity, and yup,
I can't do it:

$ git push -f upstream master
Counting objects: 111, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (54/54), done.
Writing objects: 100% (111/111), 19.58 KiB | 2.80 MiB/s, done.
Total 111 (delta 83), reused 62 (delta 56)
remote: Resolving deltas: 100% (83/83), completed with 38 local objects.
remote: FATAL: + refs/heads/master packages/sva l.collado-torres
DENIED by fallthru
remote: error: hook declined to update refs/heads/master
To git.bioconductor.org:packages/sva.git
 ! [remote rejected] master -> master (hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/sva.git'

PS2 I did push the master_backup branch to GitHub just in case we need
it later https://github.com/jtleek/sva-devel/tree/master_backup


On Sat, Aug 25, 2018 at 2:00 AM Turaga, Nitesh
 wrote:
>
> Hi Leo,
>
> I’ll try to help you with this issue.
>
> The duplicates commit you have on your package “sva” come from the pre-git 
> era of Bioconductor.  There are three ways we can fix this,
>
> 1,
>
> You fix your GitHub repo by removing the duplicate commits. They happen only 
> after this commit.
>
> commit d12b53824915f0ff7b7906043c7fc9237521e8f3
> Author: Kipper Fletez-Brant 
> Date:   Sat Apr 22 10:42:29 2017 -0400
>
> actually did it
>
>
> You can do the cherry-picking of the commits (only one from a set of 
> duplicate commits, one after the other to construct your git history). It is 
> outlined in this document here,
>
> 
> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/.
>
> If you choose this method, I can help with any questions you may have.
>
> Some help if you decide to choose this route,
>
> A.
>
> You might face issues with this commit (7e4aa44 Merge pull request 
> #26 from cafletezbrant/master) while doing the cherry-pick.
> You can ignore this, because the commits themselves will be in the 
> git history.
>
> d12b538 actually did it
> 7cedd49 needed to use tcrossprod(t(...)) a bunch
>
>
> B.
>
> If you hit a lot of merge conflicts while doing the cherry-pick, the 
> best way I’ve gotten used to is by using
>
> `git mergetool`.
>
> (I personally use the option `git mergetool -t vimdiff`, but feel 
> free to use whatever merge tool you’d like)
>
> C.
>
> Make sure you cherry-pick the RELEASE commits which come from the 
> core team while doing the cherry-pick process.
>
> 2,
>
> I can fix the bioconductor repo on my end to show no duplicate commits. Then 
> you’d have to force your Github master branch to be the same as the 
> Bioconductor repo and then put Claire’s commits on top of them. This is a 
> slightly less optimal solution because I might make some mistakes resolving 
> the conflicts, since I don’t know the details of code.
>
> 3,
>
> Since the issue of duplicate commits was pre-git era, we can just ignore the 
> duplicates. It is pretty straightforward to disable the duplicate commit 
> check, but it should only be a worst case. I don’t recommend this for your 
> repo because there are very few issues and it seems we can resolve them. I 
> reserve this option for packages which have extensively fractured their git 
> history.
>
>
> Best regards,
>
> Nitesh
>
>
> =
> Nitesh Turaga
> Bioconductor Core Team
>
>
> > On Aug 24, 2018, at 11:29 PM, Leonardo Collado Torres  
> > wrote:
> >
> > Hi,
> >
> > I'm having trouble with synching a github repo with Bioc.
> >
> > At https://github.com/jtleek/sva-devel/commits/master we have 3 recent
> > commits by Claire that we want to sync with Bioc. I followed the
> > instructions at
> > http://bioconductor.org/develop

Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

[Leonardo Collado Torres]

Thank you Nitesh!

I'll talk to Jeff and Claire.

Best,
Leo

On Sat, Aug 25, 2018 at 2:00 AM Turaga, Nitesh
 wrote:
>
> Hi Leo,
>
> I’ll try to help you with this issue.
>
> The duplicates commit you have on your package “sva” come from the pre-git 
> era of Bioconductor.  There are three ways we can fix this,
>
> 1,
>
> You fix your GitHub repo by removing the duplicate commits. They happen only 
> after this commit.
>
> commit d12b53824915f0ff7b7906043c7fc9237521e8f3
> Author: Kipper Fletez-Brant 
> Date:   Sat Apr 22 10:42:29 2017 -0400
>
> actually did it
>
>
> You can do the cherry-picking of the commits (only one from a set of 
> duplicate commits, one after the other to construct your git history). It is 
> outlined in this document here,
>
> 
> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/.
>
> If you choose this method, I can help with any questions you may have.
>
> Some help if you decide to choose this route,
>
> A.
>
> You might face issues with this commit (7e4aa44 Merge pull request 
> #26 from cafletezbrant/master) while doing the cherry-pick.
> You can ignore this, because the commits themselves will be in the 
> git history.
>
> d12b538 actually did it
> 7cedd49 needed to use tcrossprod(t(...)) a bunch
>
>
> B.
>
> If you hit a lot of merge conflicts while doing the cherry-pick, the 
> best way I’ve gotten used to is by using
>
> `git mergetool`.
>
> (I personally use the option `git mergetool -t vimdiff`, but feel 
> free to use whatever merge tool you’d like)
>
> C.
>
> Make sure you cherry-pick the RELEASE commits which come from the 
> core team while doing the cherry-pick process.
>
> 2,
>
> I can fix the bioconductor repo on my end to show no duplicate commits. Then 
> you’d have to force your Github master branch to be the same as the 
> Bioconductor repo and then put Claire’s commits on top of them. This is a 
> slightly less optimal solution because I might make some mistakes resolving 
> the conflicts, since I don’t know the details of code.
>
> 3,
>
> Since the issue of duplicate commits was pre-git era, we can just ignore the 
> duplicates. It is pretty straightforward to disable the duplicate commit 
> check, but it should only be a worst case. I don’t recommend this for your 
> repo because there are very few issues and it seems we can resolve them. I 
> reserve this option for packages which have extensively fractured their git 
> history.
>
>
> Best regards,
>
> Nitesh
>
>
> =
> Nitesh Turaga
> Bioconductor Core Team
>
>
> > On Aug 24, 2018, at 11:29 PM, Leonardo Collado Torres  
> > wrote:
> >
> > Hi,
> >
> > I'm having trouble with synching a github repo with Bioc.
> >
> > At https://github.com/jtleek/sva-devel/commits/master we have 3 recent
> > commits by Claire that we want to sync with Bioc. I followed the
> > instructions at
> > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> > and then had to do step #8 where I ran steps 1-4 from "force
> > Bioconductor master to Github master"
> > http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-.
> > On the optional step 4 I used git cherry-pick to pick the 3 commits by
> > Claire. That's how we got to the current state on the jtleek/sva-devel
> > repo (git added me as a co-author of the commits). However, "git push
> > upstream master" keeps failing as shown below:
> >
> > $ git push upstream master
> > Counting objects: 15, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (7/7), done.
> > Writing objects: 100% (15/15), 2.76 KiB | 2.76 MiB/s, done.
> > Total 15 (delta 9), reused 11 (delta 8)
> > remote: Error: duplicate commits.
> > remote:
> > remote: There are duplicate commits in your commit history, These cannot be
> > remote: pushed to the Bioconductor git server. Please make sure that this is
> > remote: resolved.
> > remote:
> > remote: Take a look at the documentation to fix this,
> > remote: 
> > https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> > remote: particularly, point #8 (force Bioconductor master to Github master).
> > remote:
> > remote: For more information, or help resolving this issue, contact
> > remote: . Provide the error, the package name and
> > remote: any other details we might need.
> > remote:
> > remote: Use
> 

[Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

[Leonardo Collado Torres]

Hi,

I'm having trouble with synching a github repo with Bioc.

At https://github.com/jtleek/sva-devel/commits/master we have 3 recent
commits by Claire that we want to sync with Bioc. I followed the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and then had to do step #8 where I ran steps 1-4 from "force
Bioconductor master to Github master"
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-.
On the optional step 4 I used git cherry-pick to pick the 3 commits by
Claire. That's how we got to the current state on the jtleek/sva-devel
repo (git added me as a co-author of the commits). However, "git push
upstream master" keeps failing as shown below:

$ git push upstream master
Counting objects: 15, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (15/15), 2.76 KiB | 2.76 MiB/s, done.
Total 15 (delta 9), reused 11 (delta 8)
remote: Error: duplicate commits.
remote:
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote:
remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote:
remote: For more information, or help resolving this issue, contact
remote: . Provide the error, the package name and
remote: any other details we might need.
remote:
remote: Use
remote:
remote: git show 812b53941d5ba3e70797e4ecfef8401b89fc4741
remote: git show a3406ad11056cc5f1896f71c7864e2c3bd80b817
remote:
remote: to see body of commits.
remote:
To git.bioconductor.org:packages/sva.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/sva.git'


If I clone g...@git.bioconductor.org:packages/sva.git I can see that
both 812b5394 and a3406ad1 already exist on the Bioc git. I see that
one of the notes at
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
mentions that the step 1-4 solution won't work in this scenario. The
"Reset to a previous commit" section recommends using git reset
--hard. But that still fails.

$ git reset -- hard a3406ad11056c
13:58 sva-devel $ git status
On branch master
Your branch is ahead of 'upstream/master' by 3 commits.
  (use "git push" to publish your local commits)

nothing to commit, working tree clean
13:58 sva-devel $ git push -f upstream master
Counting objects: 15, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (15/15), 2.76 KiB | 1.38 MiB/s, done.
Total 15 (delta 9), reused 11 (delta 8)
remote: Error: duplicate commits.
remote:
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote:
remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote:
remote: For more information, or help resolving this issue, contact
remote: . Provide the error, the package name and
remote: any other details we might need.
remote:
remote: Use
remote:
remote: git show 812b53941d5ba3e70797e4ecfef8401b89fc4741
remote: git show a3406ad11056cc5f1896f71c7864e2c3bd80b817
remote:
remote: to see body of commits.
remote:
To git.bioconductor.org:packages/sva.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/sva.git'

So hm... I have no idea how to fix this.

Best,
Leo

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: Re: Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Leonardo Collado Torres]

Sorry about that Martin. Here's my thank you reply to Hervé from August 2nd.



Thanks Hervé and no problem about the Windows binary.

Richard did get DelayedArray installed today (I think using biocLite)! ^^

Best,
Leo


On Fri, Aug 3, 2018 at 8:27 AM Martin Morgan
 wrote:
>
>
> The large number of people cc'd on this thread causes the mailman
> software to block posts. I'm removing individuals, please respond to
> this message.
>
> On 08/02/2018 01:57 PM, Hervé Pagès wrote:
> > Hi Leonardo,
> >
> > Hope you were able to solve your connection problems.
> > Just to let you that I fixed the DelayedArray timeout on
> > Windows and the zip files are now available for this
> > platform:
> >
> >https://bioconductor.org/packages/DelayedArray
> >
> > Sorry for the inconvenience.
> >
> > Cheers,
> > H.
> >
> >
> > On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
> >> Hi,
> >>
> >> Just as a quick update. Everything worked yesterday when Richard used
> >> another PC computer from his home (another network). So it's
> >> definitely not a Bioc problem.
> >>
> >> Yet I have no idea how to troubleshoot it beyond burning it all and
> >> starting from scratch: re-installing R and everything and checking if
> >> that works. Well, or testing using a hotspot wifi connection with one
> >> of our phones and seeing if that works to bypass the wifi network from
> >> work.
> >>
> >> Best,
> >> Leo
> >>
> >> On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr. 
> >> wrote:
> >>>
> >>> are you sure his tmp directory isn't full
> >>>
> >>> --t
> >>>
> >>>
> >>> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres
> >>>  wrote:
> >>>>
> >>>>  From Richard:
> >>>>
> >>>>> BiocManager::install("DelayedArray")
> >>>>
> >>>> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
> >>>>
> >>>> Installing package(s) 'BiocVersion', 'DelayedArray'
> >>>>
> >>>> trying URL
> >>>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ='
> >>>>
> >>>>
> >>>> Content type 'application/zip' length 8649 bytes
> >>>>
> >>>> downloaded 8649 bytes
> >>>>
> >>>>
> >>>>
> >>>> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
> >>>>
> >>>>
> >>>>
> >>>> The downloaded binary packages are in
> >>>>
> >>>> C:\Users\Richard
> >>>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
> >>>>
> >>>> installing the source package ‘DelayedArray’
> >>>>
> >>>>
> >>>>
> >>>> trying URL
> >>>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY='
> >>>>
> >>>>
> >>>> Content type 'application/x-gzip' length 486139 bytes (474 KB)
> >>>>
> >>>> downloaded 474 KB
> >>>>
> >>>>
> >>>>
> >>>> Error in untar2(tarfile, files, list, exdir, restore_times) :
> >>>>
> >>>>incomplete block on file
> >>>>
> >>>> In R CMD INSTALL
> >>>>
> >>>>
> >>>>
> >>>> The downloaded source packages are in
> >>>>
> >>>> ‘C:\Users\Richard
> >>>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
> >>>>
> >>>> installation path not writeable, unable to update packages: foreign,
> >>>> MASS, mgcv, survival
> >>>>
> >>>> Update old packages: 'openssl', 'stringi'
> >>>>
> >>>> Update all/some/none? [a/s/n]:
> >>>>
> >>>> 

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Leonardo Collado Torres]

Thanks Hervé and no problem about the Windows binary.

Richard did get DelayedArray installed today (I think using biocLite)! ^^

Best,
Leo

On Thu, Aug 2, 2018 at 1:59 PM Hervé Pagès  wrote:

>
> Hi Leonardo,
>
> Hope you were able to solve your connection problems.
> Just to let you that I fixed the DelayedArray timeout on
> Windows and the zip files are now available for this
> platform:
>
>https://bioconductor.org/packages/DelayedArray
>
> Sorry for the inconvenience.
>
> Cheers,
> H.
>
>
> On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
> > Hi,
> >
> > Just as a quick update. Everything worked yesterday when Richard used
> > another PC computer from his home (another network). So it's
> > definitely not a Bioc problem.
> >
> > Yet I have no idea how to troubleshoot it beyond burning it all and
> > starting from scratch: re-installing R and everything and checking if
> > that works. Well, or testing using a hotspot wifi connection with one
> > of our phones and seeing if that works to bypass the wifi network from
> > work.
> >
> > Best,
> > Leo
> >
> > On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr. 
> wrote:
> >>
> >> are you sure his tmp directory isn't full
> >>
> >> --t
> >>
> >>
> >> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres <
> lcoll...@jhu.edu> wrote:
> >>>
> >>>  From Richard:
> >>>
> >>>> BiocManager::install("DelayedArray")
> >>>
> >>> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
> >>>
> >>> Installing package(s) 'BiocVersion', 'DelayedArray'
> >>>
> >>> trying URL '
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ=
> '
> >>>
> >>> Content type 'application/zip' length 8649 bytes
> >>>
> >>> downloaded 8649 bytes
> >>>
> >>>
> >>>
> >>> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
> >>>
> >>>
> >>>
> >>> The downloaded binary packages are in
> >>>
> >>> C:\Users\Richard
> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
> >>>
> >>> installing the source package ‘DelayedArray’
> >>>
> >>>
> >>>
> >>> trying URL '
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY=
> '
> >>>
> >>> Content type 'application/x-gzip' length 486139 bytes (474 KB)
> >>>
> >>> downloaded 474 KB
> >>>
> >>>
> >>>
> >>> Error in untar2(tarfile, files, list, exdir, restore_times) :
> >>>
> >>>incomplete block on file
> >>>
> >>> In R CMD INSTALL
> >>>
> >>>
> >>>
> >>> The downloaded source packages are in
> >>>
> >>> ‘C:\Users\Richard
> >>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
> >>>
> >>> installation path not writeable, unable to update packages: foreign,
> >>> MASS, mgcv, survival
> >>>
> >>> Update old packages: 'openssl', 'stringi'
> >>>
> >>> Update all/some/none? [a/s/n]:
> >>>
> >>> n
> >>>
> >>> Warning message:
> >>>
> >>> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
> >>>
> >>>installation of package ‘DelayedArray’ had non-zero exit status
> >>>
> >>>>
> >>>
> >>>
> >>>
> >>> Also, at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_DelayedArray.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=sIiQvz3aJN2aHqxD1FLQLygGYRequcJnj2ywQlGrkds=
> >>> I don't see the tar for the Windows binary.
> >>>
> >>>
> >>>
> >>>
> >>

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Leonardo Collado Torres]

Hi,

Just as a quick update. Everything worked yesterday when Richard used
another PC computer from his home (another network). So it's
definitely not a Bioc problem.

Yet I have no idea how to troubleshoot it beyond burning it all and
starting from scratch: re-installing R and everything and checking if
that works. Well, or testing using a hotspot wifi connection with one
of our phones and seeing if that works to bypass the wifi network from
work.

Best,
Leo

On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr.  wrote:
>
> are you sure his tmp directory isn't full
>
> --t
>
>
> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres  
> wrote:
>>
>> From Richard:
>>
>> > BiocManager::install("DelayedArray")
>>
>> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
>>
>> Installing package(s) 'BiocVersion', 'DelayedArray'
>>
>> trying URL 
>> 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocVersion_3.7.4.zip'
>>
>> Content type 'application/zip' length 8649 bytes
>>
>> downloaded 8649 bytes
>>
>>
>>
>> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
>>
>>
>>
>> The downloaded binary packages are in
>>
>>C:\Users\Richard 
>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
>>
>> installing the source package ‘DelayedArray’
>>
>>
>>
>> trying URL 
>> 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DelayedArray_0.6.2.tar.gz'
>>
>> Content type 'application/x-gzip' length 486139 bytes (474 KB)
>>
>> downloaded 474 KB
>>
>>
>>
>> Error in untar2(tarfile, files, list, exdir, restore_times) :
>>
>>   incomplete block on file
>>
>> In R CMD INSTALL
>>
>>
>>
>> The downloaded source packages are in
>>
>>‘C:\Users\Richard
>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
>>
>> installation path not writeable, unable to update packages: foreign,
>> MASS, mgcv, survival
>>
>> Update old packages: 'openssl', 'stringi'
>>
>> Update all/some/none? [a/s/n]:
>>
>> n
>>
>> Warning message:
>>
>> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
>>
>>   installation of package ‘DelayedArray’ had non-zero exit status
>>
>> >
>>
>>
>>
>> Also, at http://bioconductor.org/packages/release/bioc/html/DelayedArray.html
>> I don't see the tar for the Windows binary.
>>
>>
>>
>>
>> On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr.  wrote:
>> >
>> > BiocManager::install(whatever) doesn't work?
>> >
>> > biocLite is supposed to die, you see...
>> >
>> >
>> > --t
>> >
>> >
>> > On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres  
>> > wrote:
>> >>
>> >> Hi bioc-devel,
>> >>
>> >> A co-worker of mine (Richard) tried several times to install the
>> >> DelayedArray package. We got a couple of errors but it ultimately
>> >> looks like it's an internet connection problem. The truth is that
>> >> might be something affecting us on our side since I can't access
>> >> http://www.comunidadbioinfo.org/ either but collaborators in Mexico
>> >> (cc'ed) can right now. Me (on a Mac) and Emily (on a PC) on the same
>> >> network can't access that website.
>> >>
>> >> One of the errors we saw with Richard (on a PC) was about a missing
>> >> tar block. We failed to save that error message (for what's it's
>> >> worth, that was using RStudio). We then tried again and ran into this
>> >> error:
>> >>
>> >> > ## try http:// if https:// URLs are not supported
>> >>
>> >> > source("https://bioconductor.org/biocLite.R;)
>> >>
>> >> Error in file(filename, "r", encoding = encoding) :
>> >>
>> >>   cannot open the connection
>> >>
>> >> In addition: Warning message:
>> >>
>> >> In file(filename, "r", encoding = encoding) :
>> >>
>> >>   InternetOpenUrl failed: 'A connection with the server could not be
>> >> established'
>> >>
>> >> > source("http://bioconductor.org/biocLite.R;)
>> >>
>> >> Error in file(filename, "r", encoding = encoding) :
>> >>
>> >>   cannot open the co

[Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Leonardo Collado Torres]

Hi bioc-devel,

A co-worker of mine (Richard) tried several times to install the
DelayedArray package. We got a couple of errors but it ultimately
looks like it's an internet connection problem. The truth is that
might be something affecting us on our side since I can't access
http://www.comunidadbioinfo.org/ either but collaborators in Mexico
(cc'ed) can right now. Me (on a Mac) and Emily (on a PC) on the same
network can't access that website.

One of the errors we saw with Richard (on a PC) was about a missing
tar block. We failed to save that error message (for what's it's
worth, that was using RStudio). We then tried again and ran into this
error:

> ## try http:// if https:// URLs are not supported

> source("https://bioconductor.org/biocLite.R;)

Error in file(filename, "r", encoding = encoding) :

  cannot open the connection

In addition: Warning message:

In file(filename, "r", encoding = encoding) :

  InternetOpenUrl failed: 'A connection with the server could not be
established'

> source("http://bioconductor.org/biocLite.R;)

Error in file(filename, "r", encoding = encoding) :

  cannot open the connection

In addition: Warning message:

In file(filename, "r", encoding = encoding) :

  InternetOpenUrl failed: 'A connection with the server could not be
established'

> sessionInfo()

R version 3.5.0 (2018-04-23)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 17134)



Matrix products: default



locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C   LC_TIME=English_United States.1252



attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base



loaded via a namespace (and not attached):

[1] compiler_3.5.0




On my Mac however, I can install DelayedArray.

> source('http://bioconductor.org/biocLite.R')
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite('DelayedArray')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘DelayedArray’
trying URL 
'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/DelayedArray_0.6.2.tgz'
Content type 'application/x-gzip' length 1308365 bytes (1.2 MB)
==
downloaded 1.2 MB
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1


So, I have no idea how to approach this and just wanted to double
check that things are ok from your side.


Thanks,
Leo

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Re: [Bioc-devel] BiocManager now on CRAN

[Leonardo Collado Torres]

Hi Marcel,

I noticed that https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
doesn't include the experiment data and workflow packages. I updated
mine preemptively (derfinderData and recountWorkflow).

By the way, how do I sync experiment data package updates? I forgot
how to do so. Maybe it's only via svn. I checked
http://bioconductor.org/developers/how-to/git/ and the commit in
question is 
https://github.com/leekgroup/derfinderData/commit/cc0a295a730f8f19a429f28c7b327ee15ccd1e81.
Last time I did it was in 2015.

Also, I suggest changing your grep command to:

grep -rnE "biocLite|biocValid" *

that way you can include biocValid() calls which now should be
BiocManager::valid(). I had included several of them in my package
vignettes.

Best,
Leo

On Mon, Jul 16, 2018 at 1:06 PM Gabe Becker  wrote:
>
>
> Ah, of course. I should have realized that. Makes sense. I'll get that
> fixed in devel soon.
>
> Thanks and sorry for the noise.
> ~G
>
> On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos 
> wrote:
>
> > Hi Gabe,
> >
> > Please note that we are only making changes to packages in *bioc-devel*.
> >
> > BiocManager wouldn't fail for users with earlier versions of R because
> > it doesn't apply to them. These users
> > should be using the respective bioc-release versions and consequently
> > `BiocInstaller`.
> >
> > BiocManger is currently supported only for `devel` and all /bioc-devel/
> > users have R 3.5.0 or greater going forward.
> >
> >
> > Regards,
> > Marcel
> >
> >
> > On 07/16/2018 11:51 AM, Gabe Becker wrote:
> > > Marcel et al,
> > >
> > > My genbankr package is one of the ones that mentions biocLite (in
> > > README.md, actually, not the vignette proper, but still...).
> > > Historically this was just because I had missed your email and hadn't
> > > updated it, but when I sat down to do it I ran into an issue:
> > >
> > > BiocManager, while a huge step forward, requires R >3.5.0. That is
> > > still relatively new, and my package (along with all Bioc packages
> > > from the corresponding release) works fine under 3.4.x (and previous).
> > > I'm somewhat loath to completely remove the biocLite based
> > > instructions because install.packages("BiocManager") will fail (well,
> > > not with an error, but it doesn't install anything...) for users with
> > > earlier versions of R, wherease
> > > source("http://bioconductor.org/biocLite.R;) works and gets the
> > > correct version for them IIRC.
> > The `biocLite` instructions only apply the current and previous release
> > versions of Bioconductor.
> > >
> > > Is there guidance on how to handle this issue?
> > >
> > > Thanks,
> > > ~G
> > >
> > > On Sun, Jul 15, 2018 at 10:53 AM, Marcel Ramos
> > >  > > > wrote:
> > >
> > > Hi Jason,
> > >
> > > Please check all of your package files and not just the vignette.
> > >
> > > The criteria involve a simple `grep` search of all package files for
> > > the words `biocLite` and `BiocInstaller`.
> > >
> > > ~/Bioconductor/ClusterSignificance (master) $ grep -rn "biocLite" *
> > > README.md:52:source("https://bioconductor.org/biocLite.R
> > > ")
> > > README.md:53:biocLite("ClusterSignificance")
> > > README.Rmd:45:source("https://bioconductor.org/biocLite.R
> > > ")
> > > README.Rmd:46:biocLite("ClusterSignificance")
> > >
> > > As I've mentioned in the previous emails, you can use:
> > >
> > > install.packages("BiocManager")
> > > BiocManager::install("YourPackageNameHere")
> > >
> > > to replace the source function call.
> > >
> > > You may also refer to the "Installation" section of the devel
> > > landing pages
> > > for an additional example:
> > >
> > > http://bioconductor.org/packages/devel/bioc/html/
> > ClusterSignificance.html
> > >  > ClusterSignificance.html>
> > >
> > > Best regards,
> > > Marcel
> > >
> > >
> > > On 07/14/2018 03:31 AM, Jason Serviss wrote:
> > > > Hello Marcel,
> > > >
> > > > I notice that the package I maintain, ClusterSignificance, is
> > > included
> > > > in this list although I am unsure why. In your previous mail you
> > > say:
> > > >
> > > >> After the next couple of weeks or so, we will be identifying
> > > packages in
> > > >> bioc-devel (3.8) that still
> > > >> mention BiocInstaller / biocLite.
> > > >
> > > > I don’t find any mention of BiocInstaller or biocLite in the
> > > > ClusterSignificance vignette and it is a bit unclear to me what
> > > “make
> > > > changes to their ... package code to support the use of
> > > `BiocManager`”
> > > > specifically entails. Would you mind expanding on what criteria,
> > > other
> > > > than usage of BiocInstaller or biocLite in the vignette, that might
> > > > cause packages 

[Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages

[Leonardo Collado Torres]

Hi,

Two of my Bioconductor packages (regionReport and derfinderPlot) use
ggplot2 via ggbio. Since other packages import/suggest ggbio
http://bioconductor.org/packages/release/bioc/html/ggbio.html I'm
curious if you've taken a look at the email from Hadley Wickham and
the upcoming update to ggplot2 on June 25.

That email includes:

1. Read about the changes to ggplot2 at
   https://github.com/tidyverse/ggplot2/blob/master/NEWS.md#ggplot2-2219000.
   This page includes a list of breaking changes, the reasoning behind
   them, and to how to update your code.


2. Carefully inspect the failing checks listed at the bottom of this email.


I'm not sure if some of these issues are actually from ggbio or maybe
from my own code. If you think that they are on my end, please let me
know (like if you know that ggbio runs well with the new ggplot2).

Since it might be helpful for ggbio maintainers, I'm including my
check results from Hadley at the end of this email.

Best,
Leo


## regionReport https://github.com/leekgroup/regionReport

== CHECK RESULTS 

*   checking examples ... ERROR
```
...
label: MAstyle (with options)
List of 2
 $ fig.width : num 10
 $ fig.height: num 10

   inline R code fragments

label: genomeOverview1 (with options)
List of 6
 $ message   : logi FALSE
 $ fig.width : num 7
 $ fig.height: num 9
 $ dpi   : num 300
 $ eval  : symbol nullExist
 $ echo  : symbol nullExist

Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Quitting from lines 365-366 (basicExploration.Rmd)
Error: subscript contains invalid names
Execution halted
```

*   checking re-building of vignette outputs ... WARNING
```
...
  ...
[WARNING] This document format requires a nonempty  element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'bumphunterExampleOutput.utf8'
[WARNING] This document format requires a nonempty  element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'bumphunterExampleOutput.utf8'
Warning in citation("BiocStyle") :
  no date field in DESCRIPTION file of package 'BiocStyle'
Warning in citation("biovizBase") :
  no date field in DESCRIPTION file of package 'biovizBase'
Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
  no date field in DESCRIPTION file of package
'TxDb.Hsapiens.UCSC.hg19.knownGene'
Warning in citation("DEFormats") :
  no date field in DESCRIPTION file of package 'DEFormats'
Writing 34 Bibtex entries ... OK
Results written to file 'regionReportRef.bib'
Quitting from lines 230-235 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
subscript contains invalid names
Execution halted
```

## Notes by Leo: derfinderPlot::plotOverview() seems to be the culprit
here https://github.com/leekgroup/derfinderPlot/blob/master/R/plotOverview.R.
That function ends up using autoplot() and layout_karyogram() from
ggbio. Or maybe the issue is on my end with the use of
scale_colour_manual() and scale_fill_manual().





## derfinderPlot https://github.com/leekgroup/derfinderPlot


== CHECK RESULTS 

*   checking examples ... ERROR
```
...

> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
+ annotationPackage = 'org.Hs.eg.db')
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
> annotation <- matchGenes(x = genomeRegions$regions, subject = genes)
>
> ## Make the plot
> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation,
+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop,
+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Warning in getIdeoGR(data) :
  geom(ideogram) need valid seqlengths information for accurate mapping,
 now use reduced information as ideogram...
Warning: `panel.margin` is deprecated. Please use `panel.spacing`
property instead
Error in rep(startY, each = length(yy)) :
  attempt to replicate an object of type 'language'
Calls: plotCluster ... layout_karyogram -> layout_karyogram ->
.local -> geom_arch_flip2
Execution halted
```

*   checking tests ...
```
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  5: print(e1)
  6: print(e1)
  7: .local(x, ...)
  8: layout_karyogram(obj, cytobands = cytoband, geom = NULL)
  9: layout_karyogram(obj, cytobands = cytoband, geom = NULL)
  10: .local(data, ...)
  11: geom_arch_flip2(df.tri.p2, aes(x = x, y = y, xend = xend,
yend = yend, height = height),
 color = "black", size = 0.5)

  ══ testthat results

Re: [Bioc-devel] Submit package under a Github organization

[Leonardo Collado Torres]

Hi,

I don't think that anything changes. At least, I don't remember that
being the case (I have a few packages hosted in organization
accounts).

If it does break, share the github url to bioc-devel to get more
specific feedback.

Best,
Leo

On Wed, Jun 6, 2018 at 11:52 AM, Diogo P. P. Branco
 wrote:
>
>
> Dear all,
>
> Are there any specifics for submitting a software package which I created
> under
> a Github organization I am part of? Perhaps there is something different
> regarding the SSH key? I am familiar with the package submission process
> when
> the repository is under my account.
>
> Thank you for considering my query.
>
>
> Best regards,
> --
> *Diogo P. P. Branco*
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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Re: [Bioc-devel] Suggested edits to support site posting guide

[Leonardo Collado Torres]

Hi Mike, Lori and everyone else,

I recently saw this tweet
https://twitter.com/aprilwensel/status/989248246878035972 that links
to 
https://medium.com/compassionate-coding/its-time-to-retire-rtfm-31acdfef654f#---0-162

First, I'm curious if you've read it and if you like it. Second, maybe
we could include some of it (or link to it) in the suggested changes
to the posting guide that Mike is working on.

Best,
Leo



On Fri, Apr 20, 2018 at 10:10 AM, Shepherd, Lori
 wrote:
> May I also suggested when you are satisfied with user feedback and 
> alterations to create a pull request for the website repository
>
>
> https://github.com/Bioconductor/bioconductor.org
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Michael Love 
> 
> Sent: Thursday, April 12, 2018 11:23:35 AM
> To: bioc-devel
> Subject: [Bioc-devel] Suggested edits to support site posting guide
>
> dear all,
>
> I've edited the text from the posting guide
>  to update it a
> bit.
>
> For example, some of the text still referred to the mailing list
> :
> "Compose a new message with a new subject line".
>
> Mostly, though, I wanted to emphasize posting all of their R code and
> information about the experiment, which is often missing from support site
> posts. The self-contained example with data and code is rarely possible
> because many Bioc users have large datasets that can't be shared.
>
> Curious if this is useful or if others have suggestions. The following
> link allows edits:
>
> https://docs.google.com/document/d/1baiBUYB8E02KMbaojjoo-
> tKV3Ctd9sA5lVCvwFIWquA/edit?usp=sharing
>
> best,
> Mike
>
> [[alternative HTML version deleted]]
>
> ___
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>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Bioconductor 3.7 release: 3.7 branch created

[Leonardo Collado Torres]

Awesome! Congrats and thanks to everyone involved in the new release!

Best,
Leo

On Mon, Apr 30, 2018 at 12:49 PM, Obenchain, Valerie
 wrote:
>
> The Bioconductor 3.7 branch is now ready. If all goes well over the next 24
> hours we'll announce the official release tomorrow.
>
> You have access to 2 versions of your package in git: the "release"
> and "devel" versions. The �release� branch is for bug fixes and documentation
> improvements only. The �devel� branch is where normal development should
> occur.
>
> release: Bioconductor version 3.7; R version 3.5
> devel: Bioconductor version 3.8; R version 3.5
>
> To continue using your existing clone be sure to pull the version bump and
> branch creation changes from Bioconductor.
>
> Instructions for syncing:
>
>   http://bioconductor.org/developers/how-to/git/pull-upstream-changes/
>
>   https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
> Instructions for working with the branches:
>
>   http://bioconductor.org/developers/how-to/git/
>
> If you have questions, please post them to bioc-devel at
> bioc-devel@r-project.org.
>
>
> Thanks.
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
>
> ___
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>

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Re: [Bioc-devel] Web App for SSH keys

[Leonardo Collado Torres]

Hi Valerie,

Thanks for the reply and the doc changes ^^. I added a few short replies below.

Best,
Leo

On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie
<valerie.obench...@roswellpark.org> wrote:
> Hi Leo,
>
> Great feedback, thanks.
>
> On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote:
>
> This looks great Valerie, congrats to all of those involved in making
> the web app! I hope that it leads to less questions/confusion.
>
> Here are some minor comments, mostly about including some links/docs.
>
> * Under the which packages we have access to, I noticed that it's not
> showing the experimental data packages. I guess that's because they
> are not in git yet (right?).
>
>
> All software, data experiment and workflow packages are in git. You should
> be able to see all associated with your account. One of the goals of the app
> was to make package access more transparent which could help explain why a
> `push` or `fetch` failed. We match your email to the username we have in the
> gitolite packages.conf file. When I search packages.conf I see your username
> on these packages:
>
> ~/git.bioconductor.org/admin/gitolite-admin >grep -B 1
> 'master.*collado-torres' conf/packages.conf
> repo packages/sva
> RW master = j.leek l.collado-torres
> --
> repo packages/derfinder
> RW master = l.collado-torres
> --
> repo packages/derfinderHelper
> RW master = l.collado-torres
> --
> repo packages/derfinderPlot
> RW master = l.collado-torres
> --
> repo packages/regionReport
> RW master = l.collado-torres
> --
> repo packages/recount
> RW master = l.collado-torres
> --
> repo packages/recountWorkflow
> RW master = l.collado-torres
>
>
> If there is a package missing that you should have access to let us know.
> Also let me know if this differs from the list you saw when you were logged
> in.

This matches what I saw when I logged in. The only data package I've
contributed to Bioc is derfinderData. We haven't had to make any
changes to it in a long time as you can see at
https://github.com/leekgroup/derfinderData. I don't know if that
played a role in the package not showing up on m list. My email is
there on the DESCRIPTION file though
https://github.com/leekgroup/derfinderData/blob/master/DESCRIPTION#L7.

>
>
> * Under add an ssh key, the second option mentions "username.keys
> files in your GitHub account". I hadn't heard about this before. Is
> that file made automatically by editing
> https://github.com/settings/keys? If there's a website that describes
> this in more detail, I suggest including a link to it.
>
>
> Yes, this is the standard keys file and is edited through github account
> settings.
>
> A link has been added to the github HOWTO page:
>
> https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/

I like the change, it's much clearer!

>
> * I've seen several emails where Nitesh and others ask developers to
> check their SSH key using ssh -T g...@git.bioconductor.org, so maybe
> adding a reminder there would be good. Actually, maybe just include a
> link to http://bioconductor.org/developers/how-to/git/faq/ from this
> new site. By the way, that last link is not directly available from
> http://bioconductor.org/developers/ (I think), I had to go to
> http://bioconductor.org/developers/how-to/git/ then "See other
> frequently asked questions."
>
>
> I've added a link to the FAQ.

Nice! By the way, I just noticed a typo on
http://bioconductor.org/developers/how-to/git/faq/ bullet 17:

git clone g...@git.bioconductor.org:packagse/

packagse -> packages


>
> Since the FAQ is specific to version control it probably still belongs under
> developers -> Git Source Control. Maybe we could change the title from 'See
> other frequently asked questions' to just 'FAQ' or something more obvious.


Ok! To me it's really the "Git / ssh Bioc FAQ".


>
>
> * Typo: "Which packages do I have acces to?" --> access
>
>
> Fixed.
>
>
> Valerie
>
>
>
>
> Best,
> Leo
>
> On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie
> <valerie.obench...@roswellpark.org> wrote:
>
> My last email didn't make it through to the list - trying again ...
>
>
> The Web App for managing SSH keys is now available at
>
>   https://git.bioconductor.org/BiocCredentials/
>
> Accounts have been created for all package maintainers. Note the central
> identifier, i.e., how you login is your email. This email was taken from the
> DESCRIPTION of your package or the Google Sheet if you registered a key
> there.
>
> When you first visit the App you'll need to activate your account. An
> acti

Re: [Bioc-devel] Web App for SSH keys

[Leonardo Collado Torres]

This looks great Valerie, congrats to all of those involved in making
the web app! I hope that it leads to less questions/confusion.

Here are some minor comments, mostly about including some links/docs.

* Under the which packages we have access to, I noticed that it's not
showing the experimental data packages. I guess that's because they
are not in git yet (right?).
* Under add an ssh key, the second option mentions "username.keys
files in your GitHub account". I hadn't heard about this before. Is
that file made automatically by editing
https://github.com/settings/keys? If there's a website that describes
this in more detail, I suggest including a link to it.
* I've seen several emails where Nitesh and others ask developers to
check their SSH key using ssh -T g...@git.bioconductor.org, so maybe
adding a reminder there would be good. Actually, maybe just include a
link to http://bioconductor.org/developers/how-to/git/faq/ from this
new site. By the way, that last link is not directly available from
http://bioconductor.org/developers/ (I think), I had to go to
http://bioconductor.org/developers/how-to/git/ then "See other
frequently asked questions."

* Typo: "Which packages do I have acces to?" --> access

Best,
Leo

On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie
 wrote:
>
>
> My last email didn't make it through to the list - trying again ...
>
>
> The Web App for managing SSH keys is now available at
>
>   https://git.bioconductor.org/BiocCredentials/
>
> Accounts have been created for all package maintainers. Note the central 
> identifier, i.e., how you login is your email. This email was taken from the 
> DESCRIPTION of your package or the Google Sheet if you registered a key there.
>
> When you first visit the App you'll need to activate your account. An 
> activation link will be sent to your email. Once your account is activated 
> you can login. Trying to login without activation will lead to an error.
>
> Let us know if you have any questions or problems.
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Thank you Andrzej for the info!


## Re-point (1)

Regarding my (1), I got my github repo in sync following
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and 
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
It all worked without problems. Thanks again for the great docs!


## on.bioc auto-detection

At 
https://github.com/LieberInstitute/recountWorkflow/commit/b456fbbe6ddbeda297ef03b79de9e004f28c0b97#diff-a87d0071c97357f224ad6608f837fbbfR45
I'm using

on.bioc <- knitr::opts_knit$get("rmarkdown.pandoc.to") != 'latex'

to detect automatically whether I'm rendering the output for Bioc or
not. For F1000 I'll use BiocWorkflowTools::f1000_article as the output
by calling rmarkdown::render() manually. I thought this little code
would help others who want to have a single repo for both BioC and
F1000.


## Re-point (5)

>From Lori's email that she sent today, I can see at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/recountWorkflow/malbec2-buildwebvig.html
how the final Bioc web version is being built. That is:

/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
output_format="BiocStyle:::html_fragment")' &&
/home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e
'knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd",
".buildwebvig/recountWorkflow/recount-workflow.R")'

I can see the R version being used at
http://bioconductor.org/checkResults/3.7/workflows-LATEST/index.html
although not the bioc version (that I can infer from the package
loading messages, like clusterProfiler's one). This only matters in
those 6 months when release/devel are being built on the same R
version.

Now that I have the commands and versions, if I ever see anything
weird on the rendered Bioc web version I have a way to test things
myself instead of relying on the bioc builds. Since this is a bit
different than the rest of Bioc, maybe it'd be good to document the
build commands somewhere else.



Again, let me thank all of you for your work! I'm really excited about
the new workflow build chain and how it'll simplify
maintaining/writing workflows!


Best,
Leo

On Tue, Apr 3, 2018 at 6:38 AM, Andrzej Oleś <andrzej.o...@gmail.com> wrote:
>
> Dear Leo,
>
> thanks for you inquiry. Re points 2-4: there is no need to use the token file 
> .html_output anymore. This was an intermediate solution meant for the 
> transition period to new output format. Now all workflow vignettes for the 
> the website are build using this new format, regardless the `output` setting 
> in the vignette YAML header. Note that the format set in the vignette is 
> still used to render the document distributed with the package tarball.
>
> Cheers,
> Andrzej
>
>
> On Mon, Apr 2, 2018 at 4:32 PM, Leonardo Collado Torres <lcoll...@jhu.edu> 
> wrote:
>>
>> Hi,
>>
>> Thank you for all the work in this transition Andrzej, Lori, Valerie,
>> Nitesh and Hervé!
>>
>>
>> I have a few questions about the new system.
>>
>> 1) I already had a github repo (that I manually kept in sync with the
>> subversion one) for the recountWorkflow. Should I just follow the
>> instructions at
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
>> I guess that I'll need to do this too
>> http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>
>> 2) Is repo/vignettes/.html_output still needed?
>>
>> 3) Related to (2), the .html_output file used to ignore the `output`
>> line in the vignette YAML. I got an email from Lori saying that
>> output: BiocWorkflowTools::f1000_article is not working for
>> recountWorfkflow for now (no html vignette). My guess is that the
>> `output` line now matters, and in my case, that would build a pdf file
>> which is ignored due to
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
>> in my .Rbuildignore.
>>
>> 4) Related to the last 2. What setup do you recommend so I can
>> maintain a single git repo that produces the files needed for
>> uploading them to F1000research? Before this transition, I had to
>> maintain 3 repos: the subversion one for Bioc, my git copy (well,
>> main), and another one with the files setup for F1000. At some point
>> in the past, Andrzej recommended that I use "output:
>> BiocWorkflowTools::f1000_article" to try to have all the files in 1
>> place. I imagine that I would still need some ifelse() statements for
>> sentences like the one I have at
>> https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#sessio

Re: [Bioc-devel] Suggested edits to support site posting guide

[Leonardo Collado Torres]

Hi Mike,

I just added a few comments to your google doc. Thanks for doing this!

Best,
Leo

On Thu, Apr 12, 2018 at 11:23 AM, Michael Love
 wrote:
>
>
> dear all,
>
> I've edited the text from the posting guide
>  to update it a
> bit.
>
> For example, some of the text still referred to the mailing list
> :
> "Compose a new message with a new subject line".
>
> Mostly, though, I wanted to emphasize posting all of their R code and
> information about the experiment, which is often missing from support site
> posts. The self-contained example with data and code is rarely possible
> because many Bioc users have large datasets that can't be shared.
>
> Curious if this is useful or if others have suggestions. The following
> link allows edits:
>
> https://docs.google.com/document/d/1baiBUYB8E02KMbaojjoo-
> tKV3Ctd9sA5lVCvwFIWquA/edit?usp=sharing
>
> best,
> Mike
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Hi,

Thank you for all the work in this transition Andrzej, Lori, Valerie,
Nitesh and Hervé!


I have a few questions about the new system.

1) I already had a github repo (that I manually kept in sync with the
subversion one) for the recountWorkflow. Should I just follow the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
I guess that I'll need to do this too
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-

2) Is repo/vignettes/.html_output still needed?

3) Related to (2), the .html_output file used to ignore the `output`
line in the vignette YAML. I got an email from Lori saying that
output: BiocWorkflowTools::f1000_article is not working for
recountWorfkflow for now (no html vignette). My guess is that the
`output` line now matters, and in my case, that would build a pdf file
which is ignored due to
https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
in my .Rbuildignore.

4) Related to the last 2. What setup do you recommend so I can
maintain a single git repo that produces the files needed for
uploading them to F1000research? Before this transition, I had to
maintain 3 repos: the subversion one for Bioc, my git copy (well,
main), and another one with the files setup for F1000. At some point
in the past, Andrzej recommended that I use "output:
BiocWorkflowTools::f1000_article" to try to have all the files in 1
place. I imagine that I would still need some ifelse() statements for
sentences like the one I have at
https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
I think that this question could be generalized and documented in the
Bioc website.

5) Is there anything else I should be aware of so I can reproduce any
errors? In the past, the Bioc workflow system would trigger a build
immediately after a new push, and due to the custom way workflows were
built (like .html_output), I relied on these builds to check if my
changes had worked or not: specially early on where I had issues with
figures, links to figures and figure captions.

Best,
Leo






On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori
 wrote:
>
> For now the page at
>
> https://www.bioconductor.org/help/workflows/
>
> will remain and be updated accordingly however there is discussion about 
> having this page be removed or redirected.
>
>
> In the next few days I hope to have the new landing pages up and running and 
> will make an announcement when they are live. The new changes involve having 
> a link to the workflows on the biocViews page, that will directly link to a 
> workflow package landing page (like the software, annotation, and experiment 
> package do).
>
>
> Until the release your changes will be visible in devel which will transition 
> over to the new release just as done for software packages -
>
> The workflow are built monday, wednesday, and friday and the new landing 
> pages will reflect when the package is propagated like the other types of 
> packages.
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Aaron Lun 
> 
> Sent: Sunday, April 1, 2018 2:17:09 PM
> To: Herv� Pag�s; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Workflows are now in git (and other Important 
> workflow-related changes)
>
> Thanks everybody, this is much appreciated.
>
> On that note, will the compiled workflows shown at:
>
> https://www.bioconductor.org/help/workflows/
>
> ... be updated to reflect changes in the git repositories for the
> workflows?
>
> Or will the workflow page just directly link to the landing page for
> each package? This would be very convenient, not least because it will
> avoid me having to make pull requests to the bioconductor.org
> repository every time I want to change my workflow blurb.
>
> I'm in the process of fixing and updating my various workflows, and I'm
> wondering when/how my changes will be visible to users.
>
> Cheers,
>
> Aaron
>
> On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> > To the authors/maintainers of the workflows:
> >
> >
> > Following the svn-to-git migration of the software and data
> > experiment
> > packages last summer, we've completed the migration of the workflow
> > packages.
> >
> > The canonical location for the workflow source code now is
> > git.bioconductor.org
> >
> > Please use your git client to access/maintain your workflow the same
> > way you would do it for a software or data-experiment package.
> >
> > We've also migrated the workflows to our in-house build system.
> > Starting with Bioc 3.7, the build report for the devel versions of
> > the 

Re: [Bioc-devel] Nightly builds

[Leonardo Collado Torres]

On Wed, Feb 7, 2018 at 10:36 AM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
> Hi,
>
> I try to follow all the best practices but sometimes I end up relying
> on the Bioc nightly build.
>
> Anyhow, I personally use r-travis** for quick checks to detect broken
> commits instead of running R CMD check/build on my laptop. This way I
> can submit a new commit that fixes a broken commit before the Bioc
> nightly build in about the same time as using my laptop. r-travis
> doesn't always work as Bioc might have newer versions of dependencies
> or other issues (cache, timing, installation of deps), but it helps
> most of the time. A scenario where I definitely rely on the Bioc
> nightly build is when I can't reproduce the error/warning on my
> machine (with the latest setup). For example, Windows issues***.
>
> Note that I do run a quick local test of whatever bug I'm solving, but
> I might miss how my changes affected another unit test.
>
> Best,
> Leonardo
>
> ** Example setup
> https://github.com/leekgroup/derfinderPlot/blob/master/.travis.yml
> *** You can also use r-hub for testing in other OS including Windows
> but maybe not with the R version that bioc-devel needs and/or without
> being able to set useDevel(). Example
> https://github.com/LieberInstitute/jaffelab/blob/master/.travis.yml#L17-L18
> I've only used it for that non-bioc package.

More on r-hub and Bioc https://github.com/r-hub/rhub/issues/38 which I
just found

>
> On Wed, Feb 7, 2018 at 9:51 AM, Martin Morgan
> <martin.mor...@roswellpark.org> wrote:
>>
>>
>> Bioc developers!
>>
>> I've been exploring the Bioconductor nightly builds
>>
>>   http://bioconductor.org/checkResults/
>>
>> a bit using this in-development package.
>>
>>   https://github.com/mtmorgan/BiocBuildReports
>>
>> This
>>
>>   rpt <- report()
>>   filter_recent(rpt) %>% print(n = n())
>>
>> summarizes the packages changed in the 24 hours before the current build 
>> snapshot, and their fate on the nightly builds
>>
>> > filter_recent(rpt) %>% print(n=nrow(.))
>> # A tibble: 18 x 5
>>package   buildsrc checksrc push txt
>> 
>>  1 AllelicImbalance  ERRORskipped  skipped  skipped
>>  2 ChIPpeakAnno  ERRORskipped  skipped  skipped
>>  3 GenomicScores ERRORskipped  skipped  skipped
>>  4 genphen   ERRORskipped  skipped  skipped
>>  5 metavizr  ERRORskipped  skipped  skipped
>>  6 QUBIC ERRORskipped  skipped  skipped
>>  7 Repitools OK   ERRORskipped  skipped
>>  8 rtracklayer   OK   WARNINGS UNNEEDED same version exists in 
>> interna…
>>  9 genoset   OK   WARNINGS YES  new version is higher than 
>> in …
>> 10 IRanges   OK   WARNINGS YES  new version is higher than 
>> in …
>> 11 LOLA  OK   WARNINGS YES  new version is higher than 
>> in …
>> 12 DAPAR OK   OK   UNNEEDED same version exists in 
>> interna…
>> 13 AnnotationHubData OK   OK   YES  new version is higher than 
>> in …
>> 14 BEARscc   OK   OK   YES  new version is higher than 
>> in …
>> 15 ChemmineR OK   OK   YES  new version is higher than 
>> in …
>> 16 DESeq2OK   OK   YES  new version is higher than 
>> in …
>> 17 Onassis   OK   OK   YES  new version is higher than 
>> in …
>> 18 synergyfinder OK   OK   YES  new version is higher than 
>> in …
>>
>> A couple of things strike me about this.
>>
>>   - All the packages with 'ERROR' in the buildsrc or checksrc column failed 
>> to propagate because the commit, or a previous version, does not build or 
>> check. It is not a very productive development model to push broken commits 
>> to git.bioconductor.org, especially if the developer doesn't realize that 
>> the commits are broken. The best practice is to build and check packages 
>> locally, and then commit.
>>
>>   R CMD build 
>>   R CMD check <YourPackage_.tar.gz
>>
>> An even more robust approach is to clone the repository locally, so that the 
>> build and check are against only the committed changes and not miscellaneous 
>> files or versions hanging out in your source directory
>>
>>   cd /tmp
>>   git clone /path/to/
>>   R CMD build 
>>   ...
>>
>> I would not suggest using devtools during this final stage; the build system 
>&

Re: [Bioc-devel] Nightly builds

[Leonardo Collado Torres]

Hi,

I try to follow all the best practices but sometimes I end up relying
on the Bioc nightly build.

Anyhow, I personally use r-travis** for quick checks to detect broken
commits instead of running R CMD check/build on my laptop. This way I
can submit a new commit that fixes a broken commit before the Bioc
nightly build in about the same time as using my laptop. r-travis
doesn't always work as Bioc might have newer versions of dependencies
or other issues (cache, timing, installation of deps), but it helps
most of the time. A scenario where I definitely rely on the Bioc
nightly build is when I can't reproduce the error/warning on my
machine (with the latest setup). For example, Windows issues***.

Note that I do run a quick local test of whatever bug I'm solving, but
I might miss how my changes affected another unit test.

Best,
Leonardo

** Example setup
https://github.com/leekgroup/derfinderPlot/blob/master/.travis.yml
*** You can also use r-hub for testing in other OS including Windows
but maybe not with the R version that bioc-devel needs and/or without
being able to set useDevel(). Example
https://github.com/LieberInstitute/jaffelab/blob/master/.travis.yml#L17-L18
I've only used it for that non-bioc package.

On Wed, Feb 7, 2018 at 9:51 AM, Martin Morgan
 wrote:
>
>
> Bioc developers!
>
> I've been exploring the Bioconductor nightly builds
>
>   http://bioconductor.org/checkResults/
>
> a bit using this in-development package.
>
>   https://github.com/mtmorgan/BiocBuildReports
>
> This
>
>   rpt <- report()
>   filter_recent(rpt) %>% print(n = n())
>
> summarizes the packages changed in the 24 hours before the current build 
> snapshot, and their fate on the nightly builds
>
> > filter_recent(rpt) %>% print(n=nrow(.))
> # A tibble: 18 x 5
>package   buildsrc checksrc push txt
> 
>  1 AllelicImbalance  ERRORskipped  skipped  skipped
>  2 ChIPpeakAnno  ERRORskipped  skipped  skipped
>  3 GenomicScores ERRORskipped  skipped  skipped
>  4 genphen   ERRORskipped  skipped  skipped
>  5 metavizr  ERRORskipped  skipped  skipped
>  6 QUBIC ERRORskipped  skipped  skipped
>  7 Repitools OK   ERRORskipped  skipped
>  8 rtracklayer   OK   WARNINGS UNNEEDED same version exists in 
> interna…
>  9 genoset   OK   WARNINGS YES  new version is higher than in 
> …
> 10 IRanges   OK   WARNINGS YES  new version is higher than in 
> …
> 11 LOLA  OK   WARNINGS YES  new version is higher than in 
> …
> 12 DAPAR OK   OK   UNNEEDED same version exists in 
> interna…
> 13 AnnotationHubData OK   OK   YES  new version is higher than in 
> …
> 14 BEARscc   OK   OK   YES  new version is higher than in 
> …
> 15 ChemmineR OK   OK   YES  new version is higher than in 
> …
> 16 DESeq2OK   OK   YES  new version is higher than in 
> …
> 17 Onassis   OK   OK   YES  new version is higher than in 
> …
> 18 synergyfinder OK   OK   YES  new version is higher than in 
> …
>
> A couple of things strike me about this.
>
>   - All the packages with 'ERROR' in the buildsrc or checksrc column failed 
> to propagate because the commit, or a previous version, does not build or 
> check. It is not a very productive development model to push broken commits 
> to git.bioconductor.org, especially if the developer doesn't realize that the 
> commits are broken. The best practice is to build and check packages locally, 
> and then commit.
>
>   R CMD build 
>   R CMD check 
> An even more robust approach is to clone the repository locally, so that the 
> build and check are against only the committed changes and not miscellaneous 
> files or versions hanging out in your source directory
>
>   cd /tmp
>   git clone /path/to/
>   R CMD build 
>   ...
>
> I would not suggest using devtools during this final stage; the build system 
> doesn't use devtools, as devtools has its own ideas about options etc with 
> which to build packages. The very careful would also use the build and check 
> options found on the build report of each package, e.g., from
>
>
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/rtracklayer/malbec2-buildsrc.html
>
> one might
>
>   R CMD build --keep-empty-dirs --no-resave-data rtracklayer
>
> A common problem is that packages are built and checked locally using the 
> wrong version of R and / or Bioconductor -- commits to the devel branch 
> should be against the devel version of Bioconductor and (for the current 
> release cycle) the devel version of R.
>
>   http://bioconductor.org/developers/how-to/useDevel/
>
>   - two packages (rtracklayer, DAPAR) built and checked successfully, but did 
> not propagate to the public repository. This is because they did not bump 

Re: [Bioc-devel] Missing link files in Windows (release and devel)

[Leonardo Collado Torres]

Thank you Jim! I changed it to \link[Rsamtools:BamFile-class]{BamFile}.

Best,
Leo

On Wed, Jan 17, 2018 at 11:56 AM, James W. MacDonald <jmac...@uw.edu> wrote:
>
> On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres <lcoll...@jhu.edu>
> wrote:
>>
>> Thanks Martin! I just finished fixing the links in all my packages
>> using the \link[base:cbind]{rbind} syntax. One of them did seem a bit
>> weird to me:
>>
>>  Rd warning:
>> C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqyL54j/R.INSTALL22cc280d642c/derfinder/man/loadCoverage.Rd:15:
>> missing file link 'BamFile'
>>
>> As far as I can tell, shouldn't \link[Rsamtools:BamFile]{BamFile} be
>> the same as \link[Rsamtools]{BamFile} ? On my mac the help page is
>> called BamFile, but maybe the html file on Windows has a different
>> name.
>
>
> On both my Linux  and Windows boxes it's BamFile-class.
>
> Jim
>
>
>>
>> Best,
>> Leo
>>
>> On Tue, Jan 16, 2018 at 4:58 PM, Martin Morgan
>> <martin.mor...@roswellpark.org> wrote:
>> >
>> >
>> > On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote:
>> >>
>> >> Hi,
>> >>
>> >> I have been seen warnings in several of my packages on both release
>> >> and devel only in the Windows build machines in relation to missing
>> >> link files. Is this something that I can address from my side or a
>> >> more widespread issue? If it matters, I use roxygen2 for making my Rd
>> >> files.
>> >
>> >
>> > taking the first example
>> >
>> >
>> >
>> > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences
>> >
>> > "There are two other forms of optional argument specified as
>> > \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to 
>> > files
>> > foo.html and bar.html respectively. These are rarely needed,...
>> >
>> > You have \link[base]{rbind} so R is looking for rbind.html. The file is
>> > actually cbind.html so \link[base:cbind]{rbind}. I don't know why the error
>> > is only on Windows, perhaps because html manuals are only generated on
>> > Windows?
>> >
>> > I guess the 'These are rarely needed,...' part of the manual might be
>> > informative.
>> >
>> > Martin
>> >
>> >
>> >> Best,
>> >> Leonardo
>> >>
>> >> Examples:
>> >>
>> >> Rd warning:
>> >> C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi4zjs1/R.INSTALL2e746d54e04/recount/man/geo_characteristics.Rd:17:
>> >> missing file link 'rbind'
>> >>
>> >> Rd warning:
>> >> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2NQKYR/R.INSTALL21702e4399f/regionReport/man/derfinderReport.Rd:46:
>> >> missing file link 'plotIdeogram'
>> >>
>> >> Rd warning:
>> >> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/analyzeChr.Rd:54:
>> >> missing file link 'TxDb.Hsapiens.UCSC.hg19.knownGene'
>> >>Rd warning:
>> >> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/annotateRegions.Rd:49:
>> >> missing file link 'countOverlaps'
>> >>
>> >> ___
>> >> Bioc-devel@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information.  If you are not the intended recipient(s), or the employee or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > distribution, or use of this email message is prohibited.  If you have
>> > received this message in error, please notify the sender immediately by
>> > e-mail and delete this email message from your computer. Thank you.
>> >
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099

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Re: [Bioc-devel] Missing link files in Windows (release and devel)

[Leonardo Collado Torres]

Thanks Martin! I just finished fixing the links in all my packages
using the \link[base:cbind]{rbind} syntax. One of them did seem a bit
weird to me:

 Rd warning: 
C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqyL54j/R.INSTALL22cc280d642c/derfinder/man/loadCoverage.Rd:15:
missing file link 'BamFile'

As far as I can tell, shouldn't \link[Rsamtools:BamFile]{BamFile} be
the same as \link[Rsamtools]{BamFile} ? On my mac the help page is
called BamFile, but maybe the html file on Windows has a different
name.

Best,
Leo

On Tue, Jan 16, 2018 at 4:58 PM, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
>
>
> On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I have been seen warnings in several of my packages on both release
>> and devel only in the Windows build machines in relation to missing
>> link files. Is this something that I can address from my side or a
>> more widespread issue? If it matters, I use roxygen2 for making my Rd
>> files.
>
>
> taking the first example
>
>
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences
>
> "There are two other forms of optional argument specified as \link[pkg]{foo} 
> and \link[pkg:bar]{foo} to link to the package pkg, to files foo.html and 
> bar.html respectively. These are rarely needed,...
>
> You have \link[base]{rbind} so R is looking for rbind.html. The file is 
> actually cbind.html so \link[base:cbind]{rbind}. I don't know why the error 
> is only on Windows, perhaps because html manuals are only generated on 
> Windows?
>
> I guess the 'These are rarely needed,...' part of the manual might be 
> informative.
>
> Martin
>
>
>> Best,
>> Leonardo
>>
>> Examples:
>>
>> Rd warning: 
>> C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi4zjs1/R.INSTALL2e746d54e04/recount/man/geo_characteristics.Rd:17:
>> missing file link 'rbind'
>>
>> Rd warning: 
>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2NQKYR/R.INSTALL21702e4399f/regionReport/man/derfinderReport.Rd:46:
>> missing file link 'plotIdeogram'
>>
>> Rd warning: 
>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/analyzeChr.Rd:54:
>> missing file link 'TxDb.Hsapiens.UCSC.hg19.knownGene'
>>Rd warning: 
>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/annotateRegions.Rd:49:
>> missing file link 'countOverlaps'
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
>

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[Bioc-devel] Missing link files in Windows (release and devel)

[Leonardo Collado Torres]

Hi,

I have been seen warnings in several of my packages on both release
and devel only in the Windows build machines in relation to missing
link files. Is this something that I can address from my side or a
more widespread issue? If it matters, I use roxygen2 for making my Rd
files.

Best,
Leonardo

Examples:

Rd warning: 
C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi4zjs1/R.INSTALL2e746d54e04/recount/man/geo_characteristics.Rd:17:
missing file link 'rbind'

Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2NQKYR/R.INSTALL21702e4399f/regionReport/man/derfinderReport.Rd:46:
missing file link 'plotIdeogram'

Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/analyzeChr.Rd:54:
missing file link 'TxDb.Hsapiens.UCSC.hg19.knownGene'
  Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R.INSTALL17382396f82/derfinder/man/annotateRegions.Rd:49:
missing file link 'countOverlaps'

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Re: [Bioc-devel] Data package timeouts

[Leonardo Collado Torres]

Hi Sean,

I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
Here's a quick example:

library('GEOquery')
getGEO('GSM1062236', getGPL = FALSE)

I found it from
https://github.com/leekgroup/recount/blob/master/tests/testthat/test-misc.R#L19

Best,
Leo


> library('GEOquery')
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> getGEO('GSM1062236', getGPL = FALSE)
File stored at:
/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//RtmpAyQR3U/GSM1062236.soft
## Force terminate after a long running time
^C
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
[1] GEOquery_2.46.10Biobase_2.38.0  BiocGenerics_0.24.0
[4] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14 tidyr_0.7.2  dplyr_0.7.4  assertthat_0.2.0
 [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4  bindrcpp_0.2
 [9] limma_3.34.2 xml2_1.1.1   readr_1.1.1  glue_1.2.0
[13] purrr_0.2.4  hms_0.4.0compiler_3.4.2   pkgconfig_2.0.1
[17] bindr_0.1tibble_1.3.4


On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
>
> Thanks Sean! I was seeing timeouts also in recount related to GEOquery which 
> I just recently looked into.
>
> On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis <seand...@gmail.com> wrote:
>>
>>
>> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith <grimbo...@gmail.com> wrote:
>>
>> > Thanks for the speedy response Sean.  I'll switch back to the version
>> > using a file name shortly.
>> >
>>
>> No problem. Let me know if it does not work as expected.
>>
>> Sean
>>
>>
>>
>> >
>> > Cheers,
>> > Mike
>> >
>> > On 30 November 2017 at 11:20, Sean Davis <seand...@gmail.com> wrote:
>> >
>> >> Thanks for the report, Mike.
>> >>
>> >> The problem was (specifically) in parsing a GSEMatrix file using a
>> >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
>> >> (devel).
>> >>
>> >> Sean
>> >>
>> >>
>> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith <grimbo...@gmail.com> wrote:
>> >>
>> >>> Hi Mike,
>> >>>
>> >>> I was experiencing similar problems with the BeadArrayUseCases vignette,
>> >>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
>> >>> infinite loop processing a GSE series matrix file.  It looks like both of
>> >>> your examples try to do this too, so I suspect it's a similar issue.  I
>> >>> think the format of those files has changed recently and it seems to be
>> >>> causing a fair few issues with GEOquery.
>> >>>
>> >>> I temporarily settled a solution by getting querying GEO directly rather
>> >>> than using a local file, but it would be nice to get it back working as
>> >>> intended.
>> >>>
>> >>> Mike
>> >>>
>> >>> On 29 November 2017 at 18:56, Mi

Re: [Bioc-devel] Data package timeouts

[Leonardo Collado Torres]

Thanks Sean! I was seeing timeouts also in recount related to GEOquery
which I just recently looked into.

On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:

>
> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith  wrote:
>
> > Thanks for the speedy response Sean.  I'll switch back to the version
> > using a file name shortly.
> >
>
> No problem. Let me know if it does not work as expected.
>
> Sean
>
>
>
> >
> > Cheers,
> > Mike
> >
> > On 30 November 2017 at 11:20, Sean Davis  wrote:
> >
> >> Thanks for the report, Mike.
> >>
> >> The problem was (specifically) in parsing a GSEMatrix file using a
> >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
> >> (devel).
> >>
> >> Sean
> >>
> >>
> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith 
> wrote:
> >>
> >>> Hi Mike,
> >>>
> >>> I was experiencing similar problems with the BeadArrayUseCases
> vignette,
> >>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
> >>> infinite loop processing a GSE series matrix file.  It looks like both
> of
> >>> your examples try to do this too, so I suspect it's a similar issue.  I
> >>> think the format of those files has changed recently and it seems to be
> >>> causing a fair few issues with GEOquery.
> >>>
> >>> I temporarily settled a solution by getting querying GEO directly
> rather
> >>> than using a local file, but it would be nice to get it back working as
> >>> intended.
> >>>
> >>> Mike
> >>>
> >>> On 29 November 2017 at 18:56, Michael Love <
> michaelisaiahl...@gmail.com>
> >>> wrote:
> >>>
> >>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE'
> on
> >>> > both release and devel machines (release was fine leading up to the
> >>> > Bioc release).
> >>> >
> >>> > Not sure what's the issue, I haven't changed these packages in a
> >>> > while. I checked these out and these both build fine and in ~30s on
> my
> >>> > machine (devel branch).
> >>> >
> >>> > Here are the reports for release:
> >>> >
> >>> > http://bioconductor.org/checkResults/release/data-
> >>> > experiment-LATEST/airway/malbec1-buildsrc.html
> >>> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/
> >>> > parathyroidSE/malbec1-buildsrc.html
> >>> >
> >>> > The vignettes are here:
> >>> >
> >>> > http://bioconductor.org/packages/3.6/data/experiment/
> >>> > vignettes/airway/inst/doc/airway.html
> >>> > http://bioconductor.org/packages/3.6/data/experiment/
> >>> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
> >>> >
> >>> > best,
> >>> > Mike
> >>> >
> >>> > ___
> >>> > Bioc-devel@r-project.org mailing list
> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> >
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>
> >>
> >> --
> >> Sean Davis, MD, PhD
> >> Center for Cancer Research
> >> National Cancer Institute
> >> National Institutes of Health
> >> Bethesda, MD 20892
> >> https://seandavi.github.io/
> >> https://twitter.com/seandavis12
> >>
> >
> >
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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Re: [Bioc-devel] Encoding issues with citations (Windows only)

[Leonardo Collado Torres]

Hi,

Explicitly specifying the citation worked, just like in
https://github.com/leekgroup/derfinderHelper/commit/b63f8c4119686630a5b3cf71c36b16e3e719cf89.
Here are the citations I ended up using:

S4Vectors = RefManageR::BibEntry(bibtype = 'manual', key = 'S4Vectors',
author = 'Hervé Pagès and Michael Lawrence and Patrick Aboyoun',
title = "S4Vectors: S4 implementation of vector-like and list-like objects",
year = 2017, doi = '10.18129/B9.bioc.S4Vectors')


GenomeInfoDb = RefManageR::BibEntry(bibtype = 'manual',
key = 'GenomeInfoDb',
author = 'Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès',
title = "GenomeInfoDb: Utilities for manipulating chromosome and
other 'seqname' identifiers",
year = 2017, doi = '10.18129/B9.bioc.GenomeInfoDb')

AnnotationDbi = RefManageR::BibEntry(bibtype = 'manual',
key = 'AnnotationDbi',
author = 'Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li',
title = 'AnnotationDbi: Annotation Database Interface',
year = 2017, doi = '10.18129/B9.bioc.AnnotationDbi')

SummarizedExperiment = RefManageR::BibEntry(bibtype = 'manual',
key = 'SummarizedExperiment',
author = 'Martin Morgan and Valerie Obenchain and Jim Hester and
Hervé Pagès',
title = 'SummarizedExperiment: SummarizedExperiment container',
year = 2017, doi = '10.18129/B9.bioc.SummarizedExperiment')

You can view the code nicely formatted at
https://github.com/cboettig/knitcitations/issues/103#issuecomment-337248710

Best,
Leo

On Mon, Oct 2, 2017 at 7:43 PM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
> Hi,
>
> I've been using knitcitations for a while to handle citations in HTML
> vignettes. I had been using knitcitations::read.bibtex() until I
> realized that it no longer reads the entries in the order that were
> given in the bib file**. So I made a change and it all works... except
> on Windows. I finally updated my R installation in a Windows laptop
> and saw that the problem is with encoding.
>
>
> This short code reproduces the issue:
>
> ## Load package
> library('knitcitations')
>
> ## Tries to cite, prints package name and error when it fails
> check_bib <- function() {
> xx <- sapply(bib, function(x) {
> tryCatch(citep(x), error = function(e) {
> message(paste('found an error attempting to cite', names(x)))
> print(e)
> })
> })
> }
>
>
> ## list of citations
> bib <- c(knitcitations = citation('knitcitations'),
> IRanges = citation('IRanges'),
> S4Vectors = citation('S4Vectors'))
> check_bib()
> citep(bib[['S4Vectors']])
>
> ## Error message:
> Error in nchar(aut) : invalid multibyte string, element 1
>
> ## Entry that fails
>> bib[['S4Vectors']]
> Pag<U+653C><U+3E38>s H, Lawrence M and Aboyoun P (2017). _S4Vectors:
> S4 implementation of vector-like and list-like objects_. R package
> version 0.15.10.
>
>
> I see that knitcitations::write.bibtex() uses a "?" in authors in
> situations like this which is why I didn't notice this issue before.
> From https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
> I see that 'Encoding' in the DESCRIPTION file is used for the citation
> and I do see "Encoding: UTF-8" in the S4Vectors DESCRIPTION file.
>
> I get this error with GenomeInfoDb, AnnotationDbi, S4Vectors and
> SummarizedExperiment (details and reproducibility info at
> https://gist.github.com/anonymous/a8c6374b381dc9c27f55487756cb4e1b)
> across the different vignettes I maintain. But I don't get it with
> IRanges, GenomicRanges and other packages where Hervé Pagès is an
> author (those packages cite the 2013 PLoS paper). For example, the
> IRanges package has a inst/CITATION file that uses citEntry(,
> textVersion = "Pag\\es"). So, specifying an inst/CITATION file works.
>
>> citep(bib[['IRanges']])
> [1] "(Lawrence, Huber, Pagès, et al., 2013)"
>
> I imagine that there is a way to deal with the encoding problem
> properly but I haven't been able to find it. If you have ideas on how
> I can fix this please let me know.
>
>
> Thanks!
> Leo
>
> PS I posted this information at
> https://github.com/cboettig/knitcitations/issues/103 as well.
>
>
>
>
>
>
>
> ** As you can see below read.bibtex() changes the order of the
> citations, so I can't cite them later using citep().
>
>> write.bibtex(bib, file = 'test.bib')
> Writing 3 Bibtex entries ... OK
> Results written to file 'test.bib'
>
>
> ## test.bib contents
> @Manual{boettiger2017knitcitations,
>   title = {knitcitations: Citations for 'Knitr' Markdown Files},
>   author = {Carl Boettiger},
>   year = {2017},
>   note = {R package version 1.0.8},
>   url = {https://CRAN.R-

Re: [Bioc-devel] Workflow builder failing at postprocessing step

[Leonardo Collado Torres]

Thanks for looking into this Andrzej!

On Wed, Oct 11, 2017 at 6:02 PM, Andrzej Oleś <andrzej.o...@gmail.com> wrote:
> Thanks Leo for drawing our attention to this issue. It will probably require
> some additional modifications to the postprocessing scripts in order to
> account for the now missing Mac tar balls. I will look into this.
>
> Cheers,
> Andrzej
>
> On Wed, Oct 11, 2017 at 8:09 PM, Leonardo Collado Torres <lcoll...@jhu.edu>
> wrote:
>>
>> Hi,
>>
>> I recently pushed some changes to recountWorkflow** that triggered new
>> "postprocessing" jobs by the workflow builder. The last few (#412 up
>> to 415) failed and I can see at
>>
>> http://docbuilder.bioconductor.org:8080/job/postprocessing/label=master/415/console
>> that the error is related to the retirement of the Mac workflow build
>> machine:
>>
>> + true
>> + MACREPO=/var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> + mkdir -p /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> + rm -f
>> /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4/recountWorkflow_*.tgz
>> + cp /var/lib/jenkins/repository/recountWorkflow/*.tgz
>> /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> cp: cannot stat '/var/lib/jenkins/repository/recountWorkflow/*.tgz':
>> No such file or directory
>> Build step 'Execute shell' marked build as failure
>>
>> Hopefully the Mac tar ball part can be ignored for now. I just wanted
>> to check if the recount workflow looked ok after I made some changes
>> suggested by Andrzej in another thread
>> https://stat.ethz.ch/pipermail/bioc-devel/2017-August/011444.html.
>>
>>
>> Thanks,
>> Leo
>>
>> ** Changes I made are from versions 0.99.32 to 0.99.37
>> https://github.com/LieberInstitute/recountWorkflow/commits/master
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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[Bioc-devel] Workflow builder failing at postprocessing step

[Leonardo Collado Torres]

Hi,

I recently pushed some changes to recountWorkflow** that triggered new
"postprocessing" jobs by the workflow builder. The last few (#412 up
to 415) failed and I can see at
http://docbuilder.bioconductor.org:8080/job/postprocessing/label=master/415/console
that the error is related to the retirement of the Mac workflow build
machine:

+ true
+ MACREPO=/var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
+ mkdir -p /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
+ rm -f 
/var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4/recountWorkflow_*.tgz
+ cp /var/lib/jenkins/repository/recountWorkflow/*.tgz
/var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
cp: cannot stat '/var/lib/jenkins/repository/recountWorkflow/*.tgz':
No such file or directory
Build step 'Execute shell' marked build as failure

Hopefully the Mac tar ball part can be ignored for now. I just wanted
to check if the recount workflow looked ok after I made some changes
suggested by Andrzej in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2017-August/011444.html.


Thanks,
Leo

** Changes I made are from versions 0.99.32 to 0.99.37
https://github.com/LieberInstitute/recountWorkflow/commits/master

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[Bioc-devel] Encoding issues with citations (Windows only)

[Leonardo Collado Torres]

Hi,

I've been using knitcitations for a while to handle citations in HTML
vignettes. I had been using knitcitations::read.bibtex() until I
realized that it no longer reads the entries in the order that were
given in the bib file**. So I made a change and it all works... except
on Windows. I finally updated my R installation in a Windows laptop
and saw that the problem is with encoding.


This short code reproduces the issue:

## Load package
library('knitcitations')

## Tries to cite, prints package name and error when it fails
check_bib <- function() {
xx <- sapply(bib, function(x) {
tryCatch(citep(x), error = function(e) {
message(paste('found an error attempting to cite', names(x)))
print(e)
})
})
}


## list of citations
bib <- c(knitcitations = citation('knitcitations'),
IRanges = citation('IRanges'),
S4Vectors = citation('S4Vectors'))
check_bib()
citep(bib[['S4Vectors']])

## Error message:
Error in nchar(aut) : invalid multibyte string, element 1

## Entry that fails
> bib[['S4Vectors']]
Pags H, Lawrence M and Aboyoun P (2017). _S4Vectors:
S4 implementation of vector-like and list-like objects_. R package
version 0.15.10.


I see that knitcitations::write.bibtex() uses a "?" in authors in
situations like this which is why I didn't notice this issue before.
From https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
I see that 'Encoding' in the DESCRIPTION file is used for the citation
and I do see "Encoding: UTF-8" in the S4Vectors DESCRIPTION file.

I get this error with GenomeInfoDb, AnnotationDbi, S4Vectors and
SummarizedExperiment (details and reproducibility info at
https://gist.github.com/anonymous/a8c6374b381dc9c27f55487756cb4e1b)
across the different vignettes I maintain. But I don't get it with
IRanges, GenomicRanges and other packages where Hervé Pagès is an
author (those packages cite the 2013 PLoS paper). For example, the
IRanges package has a inst/CITATION file that uses citEntry(,
textVersion = "Pag\\es"). So, specifying an inst/CITATION file works.

> citep(bib[['IRanges']])
[1] "(Lawrence, Huber, Pagès, et al., 2013)"

I imagine that there is a way to deal with the encoding problem
properly but I haven't been able to find it. If you have ideas on how
I can fix this please let me know.


Thanks!
Leo

PS I posted this information at
https://github.com/cboettig/knitcitations/issues/103 as well.







** As you can see below read.bibtex() changes the order of the
citations, so I can't cite them later using citep().

> write.bibtex(bib, file = 'test.bib')
Writing 3 Bibtex entries ... OK
Results written to file 'test.bib'


## test.bib contents
@Manual{boettiger2017knitcitations,
  title = {knitcitations: Citations for 'Knitr' Markdown Files},
  author = {Carl Boettiger},
  year = {2017},
  note = {R package version 1.0.8},
  url = {https://CRAN.R-project.org/package=knitcitations},
}

@Article{lawrence2013software,
  title = {Software for Computing and Annotating Genomic Ranges},
  author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es
and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin
Morgan and Vincent Carey},
  year = {2013},
  journal = {{PLoS} Computational Biology},
  volume = {9},
  issue = {8},
  doi = {10.1371/journal.pcbi.1003118},
  url = 
{http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
}

@Manual{pags2017s4vectors,
  title = {S4Vectors: S4 implementation of vector-like and list-like objects},
  author = {?},
  year = {2017},
  note = {R package version 0.15.10},
}


## read.bibtex() changes the order

> read.bibtex('test.bib')
[1] ? _S4Vectors: S4 implementation of vector-like and list-like
objects_. R package version 0.15.10. 2017.

[2] C. Boettiger. _knitcitations: Citations for 'Knitr' Markdown
Files_. R package version 1.0.8. 2017. https://CRAN.R-project.org/package=knitcitations>.

[3] M. Lawrence, W. Huber, H. Pagès, et al. “Software for Computing
and Annotating Genomic Ranges”. In: _PLoS Computational Biology_ 9 (8
2013). DOI:
10.1371/journal.pcbi.1003118. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118}.>

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Re: [Bioc-devel] Package DMCHMM is not installed

[Leonardo Collado Torres]

From http://bioconductor.org/developers/package-submission/

Following acceptance of a package:

Packages accepted on the tracker repository are added to the ‘devel’
branch of the Bioconductor SVN repository, with the current version
number of the accepted package.
Packages are then built by the Bioconductor nightly build process. If
the build is successful, the package has its own ‘landing page’
created, and the package is made available to users of the ‘devel’
branch of Bioconductor via biocLite().



Basically, new packages are added to bioc-devel until the next
Bioconductor version is released. At that point, the packages are then
also available on bioc-release.

On Tue, Sep 12, 2017 at 9:01 AM, Farhad Shokoohi <shoko...@icloud.com> wrote:
> Thanks but that didn’t clarify why users should install the dev version.
> Why the package is not on the page
> http://bioconductor.org/packages/release/BiocViews.html#___Software
> Sorry this is first time I submitted a package to bioconductor and I am not
> so familiar with instructions.
>
>
> On Sep 11, 2017, at 11:31 PM, Leonardo Collado Torres <lcoll...@jhu.edu>
> wrote:
>
> It's only available on bioc-devel, not bioc-release. See
> http://bioconductor.org/packages/devel/bioc/html/DMCHMM.html and
> http://bioconductor.org/developers/how-to/useDevel/
>
> On Mon, Sep 11, 2017 at 7:17 PM, Farhad Shokoohi <shoko...@icloud.com>
> wrote:
>
> Hello,
>
> I tried to install my package on a machine and it gives the following
> warning which does not make sense.
>
> source("https://bioconductor.org/biocLite.R;)
>
> Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
>
> biocLite("DMCHMM")
>
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
> Installing package(s) ‘DMCHMM’
> Old packages: 'limma'
> Update all/some/none? [a/s/n]:
> n
> Warning message:
> package ‘DMCHMM’ is not available (for R version 3.4.1)
>
>
>
>
> ———
> Farhad Shokoohi
> Assistant Professor
> Department of Mathematics & Statistics
> Concordia University
> S-LB 915-1, J.W. McConnell Building,
> 1455 De Maisonneuve W.,
> Montreal, Quebec, Canada, H3G 1M8
> Office: (514) 848-2424 ext. 4017
> Fax: (514) 848-2831
> shoko...@icloud.com
>
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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Re: [Bioc-devel] Package DMCHMM is not installed

[Leonardo Collado Torres]

It's only available on bioc-devel, not bioc-release. See
http://bioconductor.org/packages/devel/bioc/html/DMCHMM.html and
http://bioconductor.org/developers/how-to/useDevel/

On Mon, Sep 11, 2017 at 7:17 PM, Farhad Shokoohi  wrote:
> Hello,
>
> I tried to install my package on a machine and it gives the following warning 
> which does not make sense.
>
>> source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
>> biocLite("DMCHMM")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
> Installing package(s) ‘DMCHMM’
> Old packages: 'limma'
> Update all/some/none? [a/s/n]:
> n
> Warning message:
> package ‘DMCHMM’ is not available (for R version 3.4.1)
>>
>
>
> ———
> Farhad Shokoohi
> Assistant Professor
> Department of Mathematics & Statistics
> Concordia University
> S-LB 915-1, J.W. McConnell Building,
> 1455 De Maisonneuve W.,
> Montreal, Quebec, Canada, H3G 1M8
> Office: (514) 848-2424 ext. 4017
> Fax: (514) 848-2831
> shoko...@icloud.com
>
>
> [[alternative HTML version deleted]]
>
> ___
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Re: [Bioc-devel] workflow building issues on mac and windows

[Leonardo Collado Torres]

ould be able to get decent output from the
>> original Rmd file which you used for the F1000 Research submission without
>> any manual Bioc-specific modifications. Note that in principle you could
>> even leave your primary document output format as
>> `BiocWorkflowTools::f1000_article`. This is because the workflows for the
>> website are build through a call to `rmarkdown::render` by specifying a
>> custom render format, so the output format set in the document header is
>> discarded anyway; it is important only for the vignette included in the
>> package tarball. But it's also fine to use either of the formats provided by
>> BiocStyle.
>>
>> It shouldn't be necessary to use the captioner package anymore, as figure
>> numbering is now handled by bookdown. Gosia used it in cytofWorkflow before
>> I enabled the new html engine for her workflow, which I did only yesterday.
>>
>> Re the specific builder issues: I've deleted the /tmp/udcCache dir on Mac,
>> but it didn't help. I'm not sure yet what could be the problem there. The
>> citeproc conversion error on Windows might be because of the older pandoc
>> version (1.17.2), will look into this. The convert warnings appear because
>> the new BiocStyle formats set the `knitr::opts_chunk(crop=TRUE)` to crop out
>> excessive white space around plots, will try to sanitize this a little bit
>> too.
>>
>> Cheers,
>> Andrzej
>>
>> On Thu, Aug 31, 2017 at 8:15 PM, Leonardo Collado Torres
>> <lcoll...@jhu.edu> wrote:
>>>
>>> Hi,
>>>
>>> I recently got a workflow accepted and I've been trying to get the
>>> workflow builder to successfully complete on Mac and Windows which is
>>> based on bioc-release. Note that the workflow did build properly on
>>> those operating systems using the SPB (bioc-devel).
>>>
>>>
>>> ## Linux: working
>>>
>>> After looking at
>>>
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow
>>> and
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/rnaseqGene
>>> I was able to:
>>>
>>> (1) get the figure references and captions working using captioner
>>> (2) actually get the figures to show
>>> (3) use the new layout (thanks to vignettes/.html_output)
>>>
>>> Since the build completes on Linux,
>>> http://bioconductor.org/help/workflows/recountWorkflow/ is now live.
>>> Only the links to the Mac and Windows binaries fail.
>>>
>>>
>>> ## Mac: could be a permissions issue
>>>
>>> The issue with Mac is (details at
>>>
>>> http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=vagrantmac/9/console)
>>> is that I eventually run into this error:
>>>
>>> Quitting from lines 735-747 (recount-workflow.Rmd)
>>> Error: processing vignette 'recount-workflow.Rmd' failed with
>>> diagnostics:
>>> UCSC library operation failed
>>> Execution halted
>>>
>>>
>>> The referenced lines break because of:
>>>
>>> regions <- expressed_regions("SRP045638", "chr21", cutoff = 5L,
>>> maxClusterGap = 3000L)
>>>
>>> This code uses rtracklayer::import.bw() with a URL that gets
>>> forwarded. I made sure that I am requiring the latest bioc-release
>>> rtracklayer in the description file, so this leads me to think that
>>> this issue is a repeat of
>>> https://stat.ethz.ch/pipermail/bioc-devel/2016-August/009599.html
>>> where the solution involved changing some permissions. Dan stated in
>>> that thread (3rd email): "Actually it looks like it was a permissions
>>> issue with the directory /tmp/udcCache. I removed this directory (as
>>> superuser) and that error no longer happens."
>>>
>>> Does this sound like something that could be happening in the Mac
>>> builder?
>>>
>>>
>>>
>>> ## Windows: figure and pandoc-citeproc issues
>>>
>>>
>>> In Windows, I see warnings like this:
>>>
>>> Invalid Parameter - -trim
>>> Warning: running command 'C:\Windows\system32\cmd.exe /c convert
>>> "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"' had status 4
>>> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>>>   'convert "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"'
>>> execution failed with error code 4
>>>
>>

[Bioc-devel] workflow building issues on mac and windows

[Leonardo Collado Torres]

s that the Windows one has the same version. But maybe that
could be the issue. BiocStyle 2.5.15 is installed in the Linux machine
too (Bioconductor/BiocStyle@2a1ba75) which is newer than the latest
bioc-release (2.4.1), but again, I assume that the Windows machine has
the same version.



Anyhow, I haven't been able to fix these issues and was wondering if
anyone else had ideas that could resolve them. Regardless, I'm happy
that I got http://bioconductor.org/help/workflows/recountWorkflow/ up
and looking good ^^. It's just the links to the Mac/Windows
binaries...


Thank you,
Leo



** I've been pushing changes via svn, I know that workflows are not
part of the git transition. I just keep everything in sync manually
with the GitHub repo.


Leonardo Collado Torres, Ph. D., Data Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io

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Re: [Bioc-devel] Updates to BiocStyle formatting

[Leonardo Collado Torres]

Hi Andrzej,

Could you let us know when you make the change which BiocStyle version
implemented the change? That way we can update our description files.

In the meantime, I switched my vignettes to use
BiocStyle::html_document2 although I need to use figure captions and
references to take advantage of all the things html_document2 has to
offer.

Best,
Leo

On Mon, Aug 7, 2017 at 8:05 AM, Andrzej Oleś  wrote:
> Dear Bioconductor Developers,
>
> We would like that in the next release most of the vignettes which use
> BiocStyle benefit from the updated formatting introduced over the last
> year. For this, all BiocStyle format functions will be switched to the new
> style. This transition will happen on Friday, August 18.
>
>
> BiocStyle 2.0
> =
>
> The new style was developed in collaboration with a professional graphics
> designer with the aim to address some of the shortcomings of the original
> implementation (e.g., inconsistent formatting both within the document and
> across output formats; non-distinctive structuring elements, for example
> running head and figure captions). Additionally, we introduced new
> features, including:
>
> -   Common formatting regardless of input (Rnw/Rmd) and output format
> (PDF/HTML)
> -   Consistent layout providing a clear separation between content and
> structuring elements emphasized by horizontal alignment
> -   Standardized way of specifying author affiliations
> -   Cross references in R Markdown based on the bookdown syntax
> -   Support for recent additions to R Markdown (floating TOC, code folding,
> ...)
> -   Footnotes typeset as margin notes
>
> The updated style is invoked through `BiocStyle::latex2`,
> `BiocStyle::pdf_document2` and `BiocStyle::html_document2` functions. Feel
> free to have a look at some live examples, for example, at [PureCN.pdf](
> http://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/PureCN.pdf)
> (PDF from Rnw source), or [A-vsn.html](
> http://bioconductor.org/packages/devel/bioc/vignettes/vsn/inst/doc/A-vsn.html)
> (HTML from Rmd source).
>
>
> Switch to the new style
> ===
>
> To streamline the process, the transition will happen automatically by
> replacing the previous format functions by the new ones as follows.
> Functions whose name ends with "2": `BiocStyle::latex2`,
> `BiocStyle::pdf_document2` and `BiocStyle::html_document2` will be renamed
> by stripping the trailing "2" such that they replace their old
> counterparts, e.g. `BiocStyle::latex`. At the same time, the latter ones
> will be archived by appending `_old` to their names so that, for example,
> `BiocStyle:latex` will become `BiocStyle::latex_old`. Function names with
> the trailing "2" will be kept until the release as aliases. Both these and
> the "old" functions will be marked as deprecated, and made defunct after
> the release following the [Function Deprecation Guidelines](
> http://bioconductor.org/developers/how-to/deprecation/). The following list
> summarizes the changes.
>
> BiocStyle::latex  -> BiocStyle::latex_old
> BiocStyle::latex2 -> BiocStyle::latex
>
> BiocStyle::pdf_document   -> BiocStyle::pdf_document_old
> BiocStyle::pdf_document2  -> BiocStyle::pdf_document
>
> BiocStyle::html_document  -> BiocStyle::html_document_old
> BiocStyle::html_document2 -> BiocStyle::html_document
>
>
> How does this affect me?
> 
>
> Scenario 1: Already using the new style (`latex2`, `pdf_document2` or
> `html_document2`)
> ---
>
> Congratulations, thank you for test driving the new style! Once these
> functions get deprecated, please rename your BiocStyle format function
> calls by removing the trailing "2".
>
> Scenario 2: Currently using the original style (`latex`, `pdf_document` or
> `html_document`)
> ---
>
> Typically, no special action will be needed. We worked hard to provide as
> much backwards compatibility as possible, so your vignette should compile
> with the new style right out of the box. However, some vignettes might
> require some small tweaks to build after the update. This affects mostly
> PDF output because of the more complex LaTeX macro definitions and the
> additional dependencies of the new style. Should you experience any
> problems, please first make sure that the source of your vignette meets the
> guidelines described in [Bioconductor LaTeX Style 2.0](
> https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf)
> (for .Rnw vignettes) or [Authoring R Markdown Vignettes](
> https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html)
> (for .Rmd vignettes). Any remaining issues should be reported as a [GitHub
> 

[Bioc-devel] Minor doc change about update_remotes.sh

[Leonardo Collado Torres]

Hi,

I used today http://bioconductor.org/developers/how-to/git-mirrors/ for
updating https://github.com/jtleek/sva-devel and I was getting weird
results when running the update_remotes.sh script
https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh.
It wasn't until I looked at the bash code that I realized that it gets the
package name from the repo name. That seems to work most of the time, but
it didn't in this case because the repo is named sva-devel while the
Bioconductor package is named sva.

I think that if update_remotes.sh showed an error message in situations
like this one or printed the usage info, then users like me would realize
that you can type:

bash update_remotes.sh sva

(and equivalent) to make the script work.

Best,
Leo

[[alternative HTML version deleted]]

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Re: [Bioc-devel] github mirror out of sync for ensembldb

[Leonardo Collado Torres]

Hi,

Ahh, ok. What I meant was that the "master" branch in
Bioconductor-mirror is not up to date with bioc-devel. I could see
that aCGH did have a release-3.5 branch, but that the "master" branch
wasn't updated. You can see something similar for
https://github.com/Bioconductor-mirror/derfinder/branches where
https://github.com/Bioconductor-mirror/derfinder/blob/master/DESCRIPTION#L5
shows version 1.9.11 while bioc-devel's
http://bioconductor.org/packages/devel/bioc/html/derfinder.html is at
1.11.0

Basically, the equivalent of older commits like
https://github.com/Bioconductor-mirror/derfinder/commit/4687d52b8c6fda6541d2454bda1517ed2776d351
and 
https://github.com/Bioconductor-mirror/derfinder/commit/a0f94bae0270f390afc00468d953237f44722790
are missing.

Best,
Leo

On Wed, May 3, 2017 at 1:54 PM, Rainer Johannes
<johannes.rai...@eurac.edu> wrote:
>
>
>> On 3 May 2017, at 19:51, Martin Morgan <martin.mor...@roswellpark.org> wrote:
>>
>> On 05/03/2017 01:10 PM, Leonardo Collado Torres wrote:
>>> Hi,
>>>
>>> I don't think that any of the Bioconductor-mirror repos have been
>>> updated to match the current bioc-devel branch. For example, look at
>>> https://github.com/Bioconductor-mirror/aCGH/blob/master/DESCRIPTION#L4
>>> which is one of the first packages by alphabetical order. My guess is
>>> that they are working on the svn to git transition plan described at
>>> https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010691.html.
>>
>> That's not correct, the repositories should be (in general) up to date. I 
>> believe Johannes' package is current (sorry, by the time I got to it it had 
>> healed itself and I didn't respond to the list).
>>
>
> No prob. I've made an update to the package and after committing the change 
> to the Bioc svn ensembldb was synced successfully.
>
>> aCGH actually had a RELEASE_3_5 branch; I'll investigate why aCGH and at 
>> least some other packages have not been fully updated after the branch.
>>
>> Martin
>>
>>
>>>
>>> Best,
>>> Leo
>>>
>>> On Thu, Apr 27, 2017 at 6:52 AM, Rainer Johannes
>>> <johannes.rai...@eurac.edu> wrote:
>>>> Hi,
>>>>
>>>> the github mirror for ensembldb seems to be out of sync with the BioC svn, 
>>>> i.e. the DESCRIPTION in 
>>>> https://github.com/Bioconductor-mirror/ensembldb/blob/master/DESCRIPTION 
>>>> is still at version 1.99.14 while in the svn it's already 2.1.0.
>>>>
>>>> First I thought the sync is not yet finished, but the release-3.5 was 
>>>> already created on the github mirror, so I guess sync must have been stuck 
>>>> somewhere.
>>>>
>>>>
>>>>
>>>>
>>>>[[alternative HTML version deleted]]
>>>>
>>>> ___
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>>>
>>> ___
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>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential 
>> information.  If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited.  If you have 
>> received this message in error, please notify the sender immediately by 
>> e-mail and delete this email message from your computer. Thank you.
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Re: [Bioc-devel] github mirror out of sync for ensembldb

[Leonardo Collado Torres]

Hi,

I don't think that any of the Bioconductor-mirror repos have been
updated to match the current bioc-devel branch. For example, look at
https://github.com/Bioconductor-mirror/aCGH/blob/master/DESCRIPTION#L4
which is one of the first packages by alphabetical order. My guess is
that they are working on the svn to git transition plan described at
https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010691.html.

Best,
Leo

On Thu, Apr 27, 2017 at 6:52 AM, Rainer Johannes
 wrote:
> Hi,
>
> the github mirror for ensembldb seems to be out of sync with the BioC svn, 
> i.e. the DESCRIPTION in 
> https://github.com/Bioconductor-mirror/ensembldb/blob/master/DESCRIPTION is 
> still at version 1.99.14 while in the svn it's already 2.1.0.
>
> First I thought the sync is not yet finished, but the release-3.5 was already 
> created on the github mirror, so I guess sync must have been stuck somewhere.
>
>
>
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] questions about windows build execute permissions and R version dependency

[Leonardo Collado Torres]

You can also test your package on R Travis against R 3.4 as shown at
https://travis-ci.org/leekgroup/recount#L518. Just use this on your
.travis.yml file
https://github.com/leekgroup/recount/blob/master/.travis.yml#L3

On Thu, Mar 23, 2017 at 4:26 AM, Martin Morgan
 wrote:
> On 03/22/2017 11:08 PM, Alicia Schep wrote:
>>
>> Hi,
>>
>> I have a two questions about the bioconductor build and BiocCheck process
>> when submitting packages.
>>
>> 1) My submitted package ('motifmatchr') returns the following warning on
>> the Windows computer:
>>
>> Warning: file 'motifmatchr/cleanup' did not have execute permissions:
>> corrected
>>
>> How can this warning be averted?  How to give the file permission? I tried
>> fixing this issue by making the file executable on my computer-- on GitHub
>> it shows up as marked as "Executable File". This did not prevent the
>> warning though.
>
>
> It seems like you've done the right thing and R is mistaken. It's also
> irrelevant, since you have a cleanup.win file that supersedes cleanup.
> Ignore the warning.
>
>> 2) The same package also gives a warning in BiocCheck related to the
>> version of R required in DESCRIPTION.  As the package is currently hosted
>> on GitHub and tested against the current release of R using travis, I
>> would
>> like the github version to have a dependency of only R 3.3 rather than R
>> 3.4. Is it possible to have a different dependency for the R version on
>> GitHub versus on Bioconductor?
>
>
> Certainly anything is possible, e.g., creating a release branch on github
> with a different dependency, but again I'd suggest evaluating whether the
> warning is relevant in your situation, and if not ignoring it.
>
> From the Bioconductor perspective, the fact that your package builds on
> travis under an earlier version of R is unknown, so the assertion that it
> only requires R-3.3 is not supportable -- the warning tries to bring your
> version requirements into line with what we know to be true. Of course the
> assertion that it depends on a version of R > 3.4 is also not supportable.
>
> Martin
>
>>
>> Appreciate any guidance on these question.  Thanks,
>>
>> Alicia
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

[Leonardo Collado Torres]

Awesome, thanks everyone! I'm tempted to write a blog post about this
whole story.

Best,
Leo

On Wed, Mar 22, 2017 at 6:36 AM, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
> On 03/22/2017 06:17 AM, Martin Maechler wrote:
>>>>>>>
>>>>>>> Andrzej Oleś <andrzej.o...@gmail.com>
>>>>>>> on Wed, 22 Mar 2017 10:29:57 +0100 writes:
>>
>>
>> > Just for the record, on R-3.3.2 Herve's code fails with the
>> following error:
>> > Error in x[TRUE] <- new("A") :
>> > incompatible types (from S4 to logical) in subassignment type fix
>>
>> yes, (of course) and I would be interested in a small
>> reproducible example which uses _valid_ code.
>> We have seen such examples with something (more complicated
>> than, but basically like)
>>
>>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>>   M <- Matrix::Matrix(exp(0:3),2)
>>   df[1:2,1:2] <- M
>>
>> which actually calls `[<-`, and then `[<-.data.frame`  and
>> always works for me but does seg.fault (in the CRAN checks of
>> package FastImputation (on 3 of the dozen platforms,
>> https://cran.r-project.org/web/checks/check_results_FastImputation.html
>>
>> one of them is
>>
>>
>> https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64-clang/FastImputation-00check.html
>>
>> I strongly suspect this is the same bug as yours, but for a case
>> where the correct behavior is *not* giving an error.
>>
>> I have also written and shown  Herve's example  to the R-core team.
>
>
> On Linux, if I run Leonardo's or Martin's example under gctorture(TRUE) I
> see a PROTECT problem; I don't see this with Herve's code, and I don't think
> his code goes through this execution path.
>
> e.g.
>
>> library(Matrix)
>> gctorture(TRUE)
>>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>>   M <- Matrix::Matrix(exp(0:3),2)
>>   df[1:2,1:2] <- M
> Error in `[<-.data.frame`(`*tmp*`, 1:2, 1:2, value =  "dgeMatrix">) :
>   unimplemented type 'integer' in 'coerceToInteger'
>
> This is addressed in r72383.
>
> R-devel$ svn diff -c72383
> Index: src/main/array.c
> ===
> --- src/main/array.c(revision 72382)
> +++ src/main/array.c(revision 72383)
> @@ -436,8 +436,12 @@
> DispatchOrEval(call, op, "length", args, rho, , 0, 1)) {
> if (length(ans) == 1 && TYPEOF(ans) == REALSXP) {
> double d = REAL(ans)[0];
> -   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d)
> -   return coerceVector(ans, INTSXP);
> +   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d) {
> +PROTECT(ans);
> +ans = coerceVector(ans, INTSXP);
> +UNPROTECT(1);
> +return(ans);
> +}
> }
> return(ans);
>  }
>
>
> Martin Morgan
>
>
>>
>> Unfortunately, I have no platform where I can trigger the bug.
>> Martin
>>
>>
>>
>> > Cheers,
>> > Andrzej
>>
>>
>>
>> > On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
>> > martin.mor...@roswellpark.org> wrote:
>>
>> >> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>> >>
>> >>> Hi Leonardo,
>> >>>
>> >>> Thanks for hunting down and isolating that bug! I tried to
>> simplify
>> >>> your code even more and was able to get a segfault with just:
>>     >>>
>> >>> setClass("A", representation(stuff="numeric"))
>> >>> x <- logical(10)
>> >>> x[TRUE] <- new("A")
>> >>>
>> >>> I get the segfault about 50% of the time on a fresh R session on
>> Mac.
>> >>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>> >>> on El Capitan. I get the segfault on both.
>> >>>
>> >>> So it looks like a bug in the `[<-` primitive to me
>> (subassignment).
>> >>>
>> >>
>> >> Any insight from
>> >>
>> >> R -d valgrind -f herve.R
>> >>
>> >> where herve.R contains the code above?
>> >>
>> >&

Re: [Bioc-devel] Citation of an accompanying paper

[Leonardo Collado Torres]

You can include both like I do in
https://github.com/leekgroup/derfinderPlot/blob/master/inst/CITATION
which is similar to what Xie's knitr does.

On Wed, Mar 22, 2017 at 12:53 PM, Gabe Becker  wrote:
> Alina,
>
> Typically in cases like the one you describe, people want users to use the
> paper citation when citing use of the package. Whether this is what they
> "should" want is somewhat debatable, but at least it seems reasonable, as
> by using the package users are, assumedly, applying the method your package
> implements.
>
> That said, a package can (from a mechanical perspective) have list more
> than one citation in it's CITATION file. Xie's knitr does this, for example
> (seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
> returned from citation(package="knitr") ) .
>
> Whether it's good to do this, and more generally whether package users
> should be expected to cite a (theory-based) methods paper and software
> which implements the method, particularly when they are by the same author,
> is again debatable. I have my thoughts on that but it's somewhat tangential
> to your question.
>
> It might be valuable for the Bioconductor team to have guidelines/an
> official view of how to navigate these issues.
>
> Best,
> ~G
>
> On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
>> If you do not have a CITATION file, a citation is automatically generated.
>> So yes, effectively it would overwrite.  See details in R-exts.
>>
>> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega 
>> wrote:
>>
>> > Hi Monther,
>> >
>> > Thank you for your reply!
>> >
>> > Would that overwrite the package citation that currently shows up on the
>> > page though? My paper doesn't cite the Bioconductor package (as it was
>> > accepted before I had a valid link to include), it just refers to the
>> same
>> > name of the computational method. Is there a way to include both
>> citations?
>> > And if not, which one should I keep?
>> >
>> > Thanks,
>> > Alina
>> >
>> > On 21 March 2017 at 22:13, Monther Alhamdoosh 
>> > wrote:
>> >
>> > > Hi Alina,
>> > >
>> > > I think you need to add a file named CITATION in your package (usually
>> > > under the inst folder) and use bibentry as follows
>> > >
>> > > bibentry(bibtype = "Article",
>> > >
>> > >  title = "Combining multiple tools outperforms individual
>> methods
>> > > in gene set enrichment analyses",
>> > >
>> > >  author = c(person("Monther", "Alhamdoosh"),
>> > >
>> > > person("Milica", "Ng"),
>> > >
>> > > person("Nicholas", "Wilson"),
>> > >
>> > > person("Julie", "Sheridan"),
>> > >
>> > > person("Huy", "Huynh"),
>> > >
>> > > person("Michael", "Wilson"),
>> > >
>> > > person("Matthew", "Ritchie")),
>> > >
>> > >  journal = "Bioinformatics",
>> > >
>> > >  page = "414-424",
>> > >
>> > >  volume = 33,
>> > >
>> > >  number = 3,
>> > >
>> > >  year = 2017,
>> > >
>> > >  doi = "10.1093/bioinformatics/btw623")
>> > >
>> > >
>> > >
>> > > Cheers,
>> > >
>> > > Monther
>> > >
>> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega 
>> > > wrote:
>> > >
>> > >> Hi,
>> > >>
>> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
>> > >> BUMHMM
>> > >> was accepted before I submitted the package for revision at
>> > Bioconductor.
>> > >> I
>> > >> would like the package page to also hold the citation to the paper.
>> What
>> > >> is
>> > >> the best way to add this paper citation? (I cite it in the vignette,
>> but
>> > >> it
>> > >> would be nice to also have it on the main page.)
>> > >>
>> > >> Thank you,
>> > >> Alina Selega
>> > >>
>> > >> [[alternative HTML version deleted]]
>> > >>
>> > >> ___
>> > >> Bioc-devel@r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >>
>> > >
>> > >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

[Leonardo Collado Torres]

Hi bioc-devel,

This is a story about a bug that took me a long time to trace. The
behaviour was really weird, so I'm sharing the story in case this
helps others in the future. I was originally writing it to request
help, but then I was able to find the issue ^^. The story ends right
now with code that will reproduce the problem with '$<-' from
IRanges/S4Vectors.




During this Bioc cycle, frequently my package derfinder has failed to
pass R CMD check in OSX. The error is always the same when it appears
and sometimes it shows up in release, but not devel and viceversa.
Right now (3/21/2017) it's visible in both
http://bioconductor.org/checkResults/release/bioc-LATEST/derfinder/morelia-checksrc.html
and 
http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/toluca2-checksrc.html.
The end of "test-all.Rout.fail" looks like this:

Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
getSegments: segmenting
getSegments: splitting
2017-03-20 02:36:52 findRegions: smoothing
2017-03-20 02:36:52 findRegions: identifying potential segments
2017-03-20 02:36:52 findRegions: segmenting information
2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s) 16.3681899295041
2017-03-20 02:36:52 findRegions: identifying candidate regions
2017-03-20 02:36:52 findRegions: identifying region clusters
2017-03-20 02:36:52 findRegions: smoothing
2017-03-20 02:36:52 findRegions: identifying potential segments
2017-03-20 02:36:52 findRegions: segmenting information
2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s) 19.7936614060235
2017-03-20 02:36:52 findRegions: identifying candidate regions
2017-03-20 02:36:52 findRegions: identifying region clusters
2017-03-20 02:36:52 findRegions: smoothing

 *** caught segfault ***
address 0x7f87d2f917e0, cause 'memory not mapped'

Traceback:
 1: (function (y, x, cluster, weights, smoothFun, ...) {
hostPackage <- environmentName(environment(smoothFun))
requireNamespace(hostPackage)smoothed <- .runFunFormal(smoothFun,
y = y, x = x, cluster = cluster, weights = weights, ...)if
(any(!smoothed$smoothed)) {smoothed$fitted[!smoothed$smoothed]
<- y[!smoothed$smoothed]}res <- Rle(smoothed$fitted)
return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
verbose = TRUE) {if (is.null(dim(y))) y <-
matrix(y, ncol = 1)if (!is.null(weights) &&
is.null(dim(weights))) weights <- matrix(weights, ncol =
1)if (is.null(x)) x <- seq(along = y)if
(is.null(weights)) weights <- matrix(1, nrow = nrow(y),
ncol = ncol(y))Indexes <- split(seq(along = cluster), cluster)
   clusterL <- sapply(Indexes, length)smoothed <-
rep(TRUE, nrow(y))for (i in seq(along = Indexes)) {
if (verbose) if (i%%1 == 0)
cat(".")Index <- Indexes[[i]]if (clusterL[i]
>= minNum & sum(rowSums(is.na(y[Index, , drop =
FALSE])) == 0) >= minNum) {nn <-
minInSpan/length(Index)for (j in 1:ncol(y)) {
sdata <- data.frame(pos = x[Index], y = y[Index,
  j], weights = weights[Index, j])  fit <-
locfit(y ˜ lp(pos, nn = nn, h = bpSpan), data =
sdata, weights = weights, family = "gaussian",
maxk = 1)  pp <- preplot(fit, where = "data", band
= "local", newdata = data.frame(pos = x[Index]))
   y[Index, j] <- pp$trans(pp$fit)}
}else {y[Index, ] <- NA
smoothed[Index] <- FALSE}}
return(list(fitted = y, smoothed = smoothed, smoother = "locfit"))
}, verbose = TRUE, minNum = 1435)
 2: .mapply(.FUN, dots, .MoreArgs)
 3: FUN(...)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({FUN(...)}, error = handle_error)
 8: withCallingHandlers({tryCatch({FUN(...)}, error =
handle_error)}, warning = handle_warning)
 9: FUN(X[[i]], ...)
10: lapply(X, FUN, ...)
11: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
  .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
12: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
  .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
13: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
weightChunks, MoreArgs = list(smoothFun = smoothFunction,
...), BPPARAM = BPPARAM)
14: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
weightChunks, MoreArgs = list(smoothFun = smoothFunction,
...), BPPARAM = BPPARAM)
15: .smootherFstats(fstats = fstats, position = position, weights =

Re: [Bioc-devel] badges for Bioconductor package

[Leonardo Collado Torres]

This is cool! Thanks Guangchuang!

On Wed, Mar 8, 2017 at 10:18 PM, Yu, Guangchuang  wrote:
>
> Dear all,
>
> I have some simple functions to create badges for using in README or github
> pages.
>
> See ggtree project website  and
> README  as
> examples.
> I think someone may also interesting in using these badges to present
> related information, including download stats, version, *etc*.
>
> I have packed these functions to a simple package, badger, which is now
> available on CRAN. You can find examples in my github repo
> .
> Bests,
> Guangchuang
> --
> --~--~-~--~~~---~--~~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~--~~~~--~~--~--~---
>
> [[alternative HTML version deleted]]
>
> ___
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[Bioc-devel] User has issue with importing a BigWig file with rtracklayer despite having a recent openssl and latest R packages

[Leonardo Collado Torres]

Hi,

I'm trying to figure out what is going wrong in
https://support.bioconductor.org/p/93182/. Mustafa is using recount to
load a bigwig file from the web. The code in recount relies on some
code in derfinder, and the actual importing is done by
rtracklayer::import().

>From looking at the R session information reported by Mustafa I can't
tell what's wrong. He has the correct versions of rtracklayer,
derfinder and recount installed. He also has openssl and pkg-config
installed. At first I thought that he might be missing openssl since
it's not listed as a SystemRequirement in the description file of
rtracklayer/derfinder/recount. I looked back at
https://support.bioconductor.org/p/81267/ and installed the latest
openssl, made it available on my PATH and installed rtracklayer from
SVN source on both R 3.4.0 and 3.3.2. In both situations, the R code
worked for me despite the message "checking for OPENSSL... no" when
installing rtracklayer. It used to be that it would say "yes" instead
of no as you can see at
https://support.bioconductor.org/p/81267/#82142.

So, it doesn't look like it's a version issue with R packages. It's
not a problem with either the latest openssl via homebrew or other
versions https://support.bioconductor.org/p/93182/#93223. I doubt that
it's an issue specific due to his openssl version (in between the
older and newer versions I tested) or his pkg-util version. It's not
an RStudio problem either (version 1.0.136 with both R 3.3.2 and
3.4.0). Could it be an RCurl issue? Could it be that his IP is blocked
by the server hosting the BigWig file?

Anyhow, I don't know what is the source of the problem and have not
been able to reproduce it. Hopefully someone here has an idea of what
is the problem.

Best,
Leo





$ brew install --force openssl

## Edited by .bashrc with the following line:
export PATH="/usr/local/opt/openssl/bin:$PATH"

$ which openssl
/usr/local/opt/openssl/bin/openssl
$ openssl version
OpenSSL 1.0.2k  26 Jan 2017

$ svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer
 $ R CMD INSTALL rtracklayer
Loading required package: colorout
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
...

Then I was able to run without problems

> library(rtracklayer)
> x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as 
> = 'RleList')
> x
RleList of length 94
$chr1
numeric-Rle of length 248956422 with 1249470 runs
  Lengths: 1337837   366372537   4433773 1
...241324 237   53537  102837 13595
  Values : 0 1 0 1 0 1 0 1 0 1
... 1 2 1 0 1 0 1 0 1 0

$chr10
numeric-Rle of length 133797422 with 412887 runs
  Lengths: 47132371237   333 1 3 3 1 1
...37   47937   37937   21137  208237 11003
  Values : 0 1 0 1 0 1 2 3 4 5
... 1 0 1 0 1 0 1 0 1 0

$chr11
numeric-Rle of length 135086622 with 700940 runs
  Lengths:  74243 37  22178 37  22907 37699 37
1236 ... 37  66776 37  36834 37   4395 37  17340
  Values :  0  1  0  1  0  1  0  1
 0 ...  1  0  1  0  1  0  1  0

$chr11_KI270721v1_random
numeric-Rle of length 100316 with 363 runs
  Lengths:  25933717 7 129 7 1  236437
...33  804837   17237   87637   49237 47993
  Values : 0 1 0 1 2 3 2 1 0 1
... 1 0 1 0 1 0 1 0 1 0

$chr12
numeric-Rle of length 133275309 with 628862 runs
  Lengths: 1005537  410137   31610 1 1 421
...371337   26337   62337  486037 64715
  Values : 0 1 0 1 0 1 2 3 4 5
... 1 0 1 0 1 0 1 0 1 0

...
<89 more elements>
> options(width = 120)
> devtools::session_info()
Session info 
---
 setting  value
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0
 ui   AQUA
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2017-03-01

Packages 
---
 package  * version  date   source
 Biobase2.35.1   2017-02-23 Bioconductor
 BiocGenerics * 0.21.3   2017-01-12 Bioconductor
 BiocParallel   1.9.52017-01-24 Bioconductor
 Biostrings 

[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

[Leonardo Collado Torres]

Hi,

I think that a recent change in S4Vectors broke
GenomicFeatures::makeTxDbFromGFF(). I ran this code about a week ago
without problems, but it's failing now.

Best,
Leo

## Unevaluated code
library('GenomicFeatures')
library('devtools')

txdb <- 
makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
format = 'gff3', organism = 'Homo sapiens')

options(width = 120)
session_info()


## Evaluated code in R 3.4.0

> library('GenomicFeatures')
> library('devtools')
>
> txdb <- 
> makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
+ format = 'gff3', organism = 'Homo sapiens')
Import genomic features from the file as a GRanges object ... trying
URL 
'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
ftp data connection made, file length 46738343 bytes
==
downloaded 44.6 MB

Error in readGFF(filepath, version = version, columns = columns, tags = tags,  :
  function '_append_string_to_CharAEAE' not provided by package 'S4Vectors'
>
> options(width = 120)
> session_info()
Session info 
---
 setting  value
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0
 ui   AQUA
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2017-01-30

Packages 
---
 package  * version  date   source
 AnnotationDbi* 1.37.1   2017-01-13 Bioconductor
 Biobase  * 2.35.0   2016-10-23 Bioconductor
 BiocGenerics * 0.21.3   2017-01-12 Bioconductor
 BiocParallel   1.9.52017-01-24 Bioconductor
 biomaRt2.31.4   2017-01-13 Bioconductor
 Biostrings 2.43.3   2017-01-24 Bioconductor
 bitops 1.0-62013-08-17 CRAN (R 3.4.0)
 DBI0.5-12016-09-10 CRAN (R 3.4.0)
 devtools * 1.12.0   2016-12-05 CRAN (R 3.4.0)
 digest 0.6.11   2017-01-03 CRAN (R 3.4.0)
 GenomeInfoDb * 1.11.6   2016-11-17 Bioconductor
 GenomicAlignments  1.11.8   2017-01-24 Bioconductor
 GenomicFeatures  * 1.27.6   2016-12-17 Bioconductor
 GenomicRanges* 1.27.21  2017-01-20 Bioconductor
 IRanges  * 2.9.16   2017-01-28 cran (@2.9.16)
 lattice0.20-34  2016-09-06 CRAN (R 3.4.0)
 Matrix 1.2-82017-01-20 CRAN (R 3.4.0)
 memoise1.0.02016-01-29 CRAN (R 3.4.0)
 Rcpp   0.12.9   2017-01-14 CRAN (R 3.4.0)
 RCurl  1.95-4.8 2016-03-01 CRAN (R 3.4.0)
 Rsamtools  1.27.12  2017-01-24 Bioconductor
 RSQLite1.1-22017-01-08 CRAN (R 3.4.0)
 rtracklayer1.35.1   2016-10-29 Bioconductor
 S4Vectors* 0.13.11  2017-01-28 cran (@0.13.11)
 SummarizedExperiment   1.5.32016-11-11 Bioconductor
 withr  1.0.22016-06-20 CRAN (R 3.4.0)
 XML3.98-1.5 2016-11-10 CRAN (R 3.4.0)
 XVector0.15.1   2017-01-24 Bioconductor
 zlibbioc   1.21.0   2016-10-23 Bioconductor
>


## Evaluate code in 3.3.2

> library('GenomicFeatures')
> library('devtools')
>
> txdb <- 
> makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
+ format = 'gff3', organism = 'Homo sapiens')
Import genomic features from the file as a GRanges object ... trying
URL 
'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
ftp data connection made, file length 46738343 bytes
==
downloaded 44.6 MB

OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to
DBI::dbGetQuery(params = bind.data).
2: Named parameters not used in query: internal_chrom_id, chrom,
length, is_circular
3: Named parameters not used in query: internal_id, name, type, chrom,
strand, start, end
4: Named parameters not used in query: internal_id, name, chrom,
strand, start, end
5: Named parameters not used in query: internal_id, name, chrom,
strand, start, end
6: Named parameters not used in query: internal_tx_id, exon_rank,
internal_exon_id, internal_cds_id
7: Named parameters not used in query: gene_id, internal_tx_id
>
> options(width = 120)
> session_info()
Session info 
---
 setting  value
 version  R version 3.3.2 RC (2016-10-26 r71594)
 system   x86_64, darwin13.4.0
 ui   X11
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2017-01-30

Packages 

Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

[Leonardo Collado Torres]

Hi Stian,

Install BiocStyle 2.3.20 or newer and that error will go away. See
https://github.com/Bioconductor/BiocStyle/issues/20 for details.

Best,
Leo

On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad  wrote:
> Hi,
>
> Could someone please advice me on the errors I'm getting building my
> package? I'm unable to reproduce them locally.
>
> Link to build report:
> http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html
> Link to bioconductor submission issue:
> https://github.com/Bioconductor/Contributions/issues/206
>
> I'm getting an error on creating my vignette: `argumemt is not a character
> vector`
> I also get this: `there is no package called 'webshot'`
>
> I believe these could be related to this warning: `Warning in
> engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3)
> and/or pandoc-citeproc not available. Falling back to R Markdown v1.`
>
> I use rmarkdown_1.2 locally without problems. Can someone here assist me?
>
> Thank you.
>
> --
> Stian Lågstad
> +47 41 80 80 25
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Leonardo Collado Torres]

Dear Jurat,

Maybe it'll be helpful to you if you see how other packages have their
data. For example, take a look at one of my packages:
https://github.com/lcolladotor/derfinder

You'll see that I have two directories inside /inst/extdata with some
files that I use in my vignette code. See
https://github.com/lcolladotor/derfinder/tree/master/inst/extdata for
the files and search system.file() inside
https://github.com/lcolladotor/derfinder/blob/master/vignettes/derfinder-quickstart.Rmd
to see how I use it in the vignette.

Regarding your permissions issue, I don't recall right now how to get
this to work with Windows. But basically you can see that error at:

Warning in dir.create(pkgoutdir, mode = "0755") :
  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason 'Permission denied'


Is your user in your windows machine part of the "administrators"
group? If not, that could be why. You could otherwise run R CMD build
and upload your tar ball (a .tar.gz file) to
https://builder.r-hub.io/.

Finally, you might want to search the manual of how to create R
extensions for other details.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html


Best,
Leo

On Fri, Dec 2, 2016 at 12:11 PM, Jurat Shayidin  wrote:
> Dear Dan :
>
> I forgot to commit vignette file,  now I pushed new changes, so now error
> could be something else. People in stackoverflow suggest me to put all my
> external data (a.k.a, bed files) into vignette folder, try to run R CMD
> check and see what happen, I did this solution, but it doesn't work. Plus,
> I checked file permission of my package parent directory, seems fine to me.
> How I check file permission of my package ?
> How can I fix this write permission on my machine ? This is not intuitive
> to me, Any hint please ?
>
> Herve suggest me don't create inst/extdata directory manually, but I still
> can't let external data available for vignette code. FYI, my objective in
> vignette file : let external data available for package use, compile
> trivial version of vignette with no error, then continue to make it
> perfect.  Here is updated session of R CMD check :
>
>
> Microsoft Windows [Version 6.3.9600]
> (c) 2013 Microsoft Corporation. All rights reserved.
>
> C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
>
> C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> "C:\Users\jvrat\Documents\MSPC"
> * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> * installing *source* package 'MSPC' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (MSPC)
>
> C:\Program Files\R\R-devel\bin\x64>R CMD check
> "C:\Users\jvrat\Documents\MSPC"
> Warning in dir.create(pkgoutdir, mode = "0755") :
>   cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
> reason 'Permission denied'
> ERROR: cannot create check dir 'C:/Program
> Files/R/R-devel/bin/x64/MSPC.Rcheck'
>
> C:\Program Files\R\R-devel\bin\x64>R CMD build
> "C:\Users\jvrat\Documents\MSPC"
> * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
> * preparing 'MSPC':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ...Warning: running command
> '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
> "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
>  ERROR
> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>   Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
> R Markdown v1.
> Quitting from lines 60-64 (vignette.Rmd)
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> subscript out of bounds
> Execution halted
>
> C:\Program Files\R\R-devel\bin\x64>
>
>
> How I fix R CMD check error above ? system.file() still can't detect
> external data. Any idea please ? Thanks a lot
>
> Best regards :
>
> Jurat
>
>
> On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum 
> wrote:
>
>> See below.
>>
>> - Original Message -
>> > From: "Jurat Shayidin" 
>> > To: "Dan Tenenbaum" , "bioc-devel" <
>> bioc-devel@r-project.org>
>> > Sent: Friday, December 2, 2016 8:32:35 AM
>> > Subject: Re: [Bioc-devel] package vignette error : external data can't
>> be captured when compiling package vignette
>>
>> > Dear Dan :
>> >
>> > Really appreciated for your quick respond. Instead, I am using R CMD
>> check
>> > on my packages, I have an error. Here is whole session detail :
>> >
>> > Microsoft Windows [Version 6.3.9600]
>> > (c) 2013 Microsoft Corporation. All rights reserved.
>> >
>> > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
>> >
>> > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
>> > "C:\Users\jvrat\Documents\MSPC"
>> > * installing to library 

Re: [Bioc-devel] Error processing scater vignette Mac OS X Sierra

[Leonardo Collado Torres]

Hi Davis,

Update your BiocStyle package to 2.2.1 (release) or 2.3.12 (devel)
which I see you are using at
https://github.com/Bioconductor-mirror/scater/blob/master/DESCRIPTION#L24.
See https://stat.ethz.ch/pipermail/bioc-devel/2016-November/010168.html
for details

Best,
Leo

On Wed, Nov 30, 2016 at 12:33 PM, Davis McCarthy  wrote:
> Hi all
>
>
>
> Since updating to Mac OS X Sierra (the only system change I can think of),
> building the vignette in scater throws an error. It seems to be caused by
> excess arguments to pandoc, but this has never been a problem until now (the
> vignette hasn't changed in any major way for months).
>
>
>
> Has anyone else seen this? Do you know how to fix?
>
>
>
> Details (error messages, session info etc) below.
>
>
>
> Best
> Davis
>
>
>
> The error message reads:
> ```
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> unused arguments (self_contained, lib_dir, output_dir)
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
> ```
>
>
>
> Running the vignette outside of R CMD check runs fine until the final step of
> converting the .md file to html, which fails with the  same error as above:
>
> ```
>
> Error in rmarkdown:::pandoc_html_highlight_args(highlight, template =
> "default",  :
>  unused arguments (self_contained, lib_dir, output_dir)
> Calls:  ->  -> overlay -> 
> Execution halted
>
> ```
>
>
>
> Unfortunately there's not really enough information there for me to know
> what's going on.
>
>
>
> Session Info:
>
> ```
>
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: macOS Sierra 10.12.1
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.8  vipor_0.4.4  plyr_1.8.4
> zlibbioc_1.20.0  viridis_0.3.4
> [6] bitops_1.0-6 tools_3.3.2  biomaRt_2.30.0
> digest_0.6.10rhdf5_2.18.0
> [11] RSQLite_1.0.0tibble_1.2   gtable_0.2.0
> lattice_0.20-34  shiny_0.14.2
> [16] DBI_0.5-1parallel_3.3.2   beeswarm_0.2.3
> gridExtra_2.2.1  stringr_1.1.0
> [21] dplyr_0.5.0  scater_1.1.27S4Vectors_0.12.0
> IRanges_2.8.1stats4_3.3.2
> [26] locfit_1.5-9.1   grid_3.3.2   shinydashboard_0.5.3
> Biobase_2.34.0   data.table_1.9.6
> [31] R6_2.2.0 AnnotationDbi_1.36.0 XML_3.98-1.5
> ggbeeswarm_0.5.0 limma_3.30.4
> [36] reshape2_1.4.2   ggplot2_2.2.0magrittr_1.5
> edgeR_3.16.3 matrixStats_0.51.0
> [41] scales_0.4.1 htmltools_0.3.5  BiocGenerics_0.20.0
> tximport_1.2.0   assertthat_0.1
> [46] mime_0.5 xtable_1.8-2 colorspace_1.3-1
> httpuv_1.3.3 stringi_1.1.2
> [51] RCurl_1.95-4.8   lazyeval_0.2.0   munsell_0.4.3
> rjson_0.2.15 chron_2.3-47
>
> ```
>
>
>
> Output of R CMD check in RStudio:
>
> ```
>
> ==> devtools::check()
>
> Updating scater documentation
> Loading scater
> Loading required package: Biobase
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
>clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>clusterExport, clusterMap, parApply, parCapply, parLapply,
>parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
>IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
>anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
>is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
>paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
>Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
>unique, unsplit, which, which.max, which.min
>
> Welcome to Bioconductor
>
>Vignettes contain introductory material; view with
>'browseVignettes()'. To cite Bioconductor, see
>'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: ggplot2
> Creating a new generic function for ‘mutate’ in package ‘scater’
> Creating a new generic function for ‘filter’ in package ‘scater’
> Setting env vars
> ---
> CFLAGS  : -Wall -pedantic
> CXXFLAGS: -Wall -pedantic
> Building scater
> 
> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
> \
>  \--no-save --no-restore --quiet CMD build  \
>  '/Users/davis/Dropbox/Projects/scater' --no-resave-data --no-manual
>
> * checking for file ‘/Users/davis/Dropbox/Projects/scater/DESCRIPTION’ ... OK
> * 

[Bioc-devel] Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

[Leonardo Collado Torres]

Hi,

The latest build report for derfinderPlot (1.9.2) shows the following error:

Quitting from lines 188-190 (derfinderPlot.Rmd)
Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics:
could not find function "aes"

I traced it down to biovizBase::parseArgsForAes() as shown below:

## evaluated code

> library('biovizBase')
> args <- alist(a = color, b = "b")
> parseArgsForAes(args)
Error in parseArgsForAes(args) : could not find function "aes"
> traceback()
1: parseArgsForAes(args)
>
> library('ggplot2')
> parseArgsForAes(args)
* NULL ->
>
> library('devtools')
> options(width = 120)
> session_info()
Session info 
---
 setting  value
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0
 ui   AQUA
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2016-11-23

Packages 
---
 package* version  date   source
 acepack  1.4.12016-10-29 CRAN (R 3.4.0)
 AnnotationDbi1.37.0   2016-10-26 Bioconductor
 AnnotationHub2.7.62016-11-19 Bioconductor
 assertthat   0.1  2013-12-06 CRAN (R 3.4.0)
 Biobase  2.35.0   2016-10-23 Bioconductor
 BiocGenerics 0.21.0   2016-10-23 Bioconductor
 BiocInstaller1.25.2   2016-10-25 Bioconductor
 BiocParallel 1.9.22016-11-18 Bioconductor
 biomaRt  2.31.1   2016-10-23 Bioconductor
 Biostrings   2.43.1   2016-11-17 Bioconductor
 biovizBase * 1.23.1   2016-10-29 Bioconductor
 bitops   1.0-62013-08-17 CRAN (R 3.4.0)
 BSgenome 1.43.1   2016-11-11 Bioconductor
 chron2.3-47   2015-06-24 CRAN (R 3.4.0)
 cluster  2.0.52016-10-08 CRAN (R 3.4.0)
 colorspace   1.3-12016-11-18 CRAN (R 3.4.0)
 data.table   1.9.62015-09-19 CRAN (R 3.4.0)
 DBI  0.5-12016-09-10 CRAN (R 3.4.0)
 devtools   * 1.12.0   2016-06-24 CRAN (R 3.4.0)
 dichromat2.0-02013-01-24 CRAN (R 3.4.0)
 digest   0.6.10   2016-08-02 CRAN (R 3.4.0)
 ensembldb1.99.3   2016-11-15 Bioconductor
 foreign  0.8-67   2016-09-13 CRAN (R 3.4.0)
 Formula  1.2-12015-04-07 CRAN (R 3.4.0)
 GenomeInfoDb 1.11.6   2016-11-17 Bioconductor
 GenomicAlignments1.11.3   2016-11-17 Bioconductor
 GenomicFeatures  1.27.2   2016-11-11 Bioconductor
 GenomicRanges1.27.12  2016-11-17 Bioconductor
 ggplot2* 2.2.02016-11-11 CRAN (R 3.4.0)
 gridExtra2.2.12016-02-29 CRAN (R 3.4.0)
 gtable   0.2.02016-02-26 CRAN (R 3.4.0)
 Hmisc4.0-02016-11-01 CRAN (R 3.4.0)
 htmlTable1.7  2016-10-19 CRAN (R 3.4.0)
 htmltools0.3.52016-03-21 CRAN (R 3.4.0)
 httpuv   1.3.32015-08-04 CRAN (R 3.4.0)
 httr 1.2.12016-07-03 CRAN (R 3.4.0)
 interactiveDisplayBase   1.13.0   2016-10-23 Bioconductor
 IRanges  2.9.82016-11-12 Bioconductor
 knitr1.15.1   2016-11-22 CRAN (R 3.4.0)
 lattice  0.20-34  2016-09-06 CRAN (R 3.4.0)
 latticeExtra 0.6-28   2016-02-09 CRAN (R 3.4.0)
 lazyeval 0.2.02016-06-12 CRAN (R 3.4.0)
 magrittr 1.5  2014-11-22 CRAN (R 3.4.0)
 Matrix   1.2-7.1  2016-09-01 CRAN (R 3.4.0)
 memoise  1.0.02016-01-29 CRAN (R 3.4.0)
 mime 0.5  2016-07-07 CRAN (R 3.4.0)
 munsell  0.4.32016-02-13 CRAN (R 3.4.0)
 nnet 7.3-12   2016-02-02 CRAN (R 3.4.0)
 plyr 1.8.42016-06-08 CRAN (R 3.4.0)
 ProtGenerics 1.7.02016-10-23 Bioconductor
 R6   2.2.02016-10-05 CRAN (R 3.4.0)
 RColorBrewer 1.1-22014-12-07 CRAN (R 3.4.0)
 Rcpp 0.12.8   2016-11-17 CRAN (R 3.4.0)
 RCurl1.95-4.8 2016-03-01 CRAN (R 3.4.0)
 rpart4.1-10   2015-06-29 CRAN (R 3.4.0)
 Rsamtools1.27.2   2016-10-23 Bioconductor
 RSQLite  1.0.02014-10-25 CRAN (R 3.4.0)
 rtracklayer  1.35.1   2016-10-29 Bioconductor
 S4Vectors0.13.2   2016-11-09 Bioconductor
 scales   0.4.12016-11-09 CRAN (R 3.4.0)
 shiny0.14.2   2016-11-01 CRAN (R 3.4.0)
 stringi  1.1.22016-10-01 CRAN (R 3.4.0)
 stringr  1.1.02016-08-19 CRAN (R 3.4.0)
 SummarizedExperiment 1.5.32016-11-11 Bioconductor
 

Re: [Bioc-devel] BiocStyle issue

[Leonardo Collado Torres]

Guangchuang, you can see at
https://github.com/Bioconductor/BiocStyle/issues/19 (the main github
repo for this package) that this issue is already been reported and
will be addressed asap by BiocStyle's maintainer.

On Tue, Nov 22, 2016 at 9:46 PM, Yu, Guangchuang  wrote:
>
> Dear all,
>
> I recompile my package and it throw the following error when building
> vignettes:
>
> unused arguments (self_contained, lib_dir, output_dir)
>
> I search  ?opts_knit, and couldn't find these parameters.
>
> In ?opts_knit, I find *self.contained* instead of *self_contained*.
>
> I remove the dependency of BiocStyle and recompile my package and it works.
>
>
> I search the source code of BiocStyle, and find the issue in
>
> https://github.com/Bioconductor-mirror/BiocStyle/blob/master/R/html_document.R#L66-L70
>
> Now rmarkdown:::pandoc_html_highlight_args (in latest release version 1.2)
> only accepts template and highlight parameters.
>
> This will fail the compilation of many Bioconductor packages. Please fix it.
>
> Using ::: is not recommended by Bioconductor and will not passed by
> BiocCheck (if I remember it correctly). But I find several packages by
> Bioconductor core team use it.
>
> Best wishes,
> Guangchuang
> --
> --~--~-~--~~~---~--~~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~--~~~~--~~--~--~---
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] Coverage test badge not updating

[Leonardo Collado Torres]

Hi Valerie,

Thanks! I do see the badges now but the percent reported seems off.
Particularly:

* http://bioconductor.org/packages/release/bioc/html/recount.html shows a
65% badge with a link to
https://codecov.io/github/Bioconductor-mirror/recount?branch=release-3.4
which has a 97% coverage
* http://bioconductor.org/packages/devel/bioc/html/recount.html shows the
correct percent in the badge (matching
https://codecov.io/github/Bioconductor-mirror/recount?branch=master )

It could be related to recount failing the latest build report on release.
Or maybe it's another alphabetical bug because the derfinder* packages look
ok.

Best,
Leo

On Fri, Nov 18, 2016 at 9:12 AM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Coverage is now up and running for the release packages. I think all
> looks well... let me know if you see any problems.
>
> Valerie
>
>
> On 11/01/2016 03:14 PM, Hervé Pagès wrote:
> > Hi Leo,
> >
> > I can confirm that while Bioc 3.4 was in devel, package coverage was
> > computed only for the devel version of packages. When we released
> > BioC 3.4, I moved the compute_coverage script that used to run on
> > zin1 (which used to be the central build node for BioC 3.4 for months)
> > to malbec2, which is the central build node for BioC 3.5.
> >
> > So yes, package coverage is still only computed for devel packages
> > at the moment. We'll see if we can restore package coverage for
> > release. If, for whatever reason, this is not possible or is too
> > complicated, we'll remove the badges from the release landing pages.
> >
> > Thanks for the reminder!
> >
> > Cheers,
> > H.
> >
> > On 11/01/2016 12:18 PM, Leonardo Collado Torres wrote:
> >> Hi,
> >>
> >> I know that there are several old threads about the coverage badges
> >> including this thread. Basically, while Bioc 3.4 was in devel, the
> >> coverage badges didn't work for Bioc release (3.3). However, now that
> >> 3.4 has been released, the badges for Bioc-release (3.4) are still not
> >> working and they only work for Bioc-devel (3.5).
> >>
> >> In one of the threads, Dan mentioned that something at codecov had
> >> changed and that he was going to ask for advice on how to proceed. I'm
> >> just curious if there are any updates on this issue. If it's only
> >> possible to have the coverage badges work for one branch, then it
> >> might be best to leave them in Bioc-devel (given Jim's arguments
> >> earlier) and remove them from Bioc-release.
> >>
> >> Best,
> >> Leo
> >>
> >> On Mon, Nov 23, 2015 at 4:25 PM, Leonardo Collado Torres
> >> <lcoll...@jhu.edu> wrote:
> >>> Thank you for fixing this Jim! I noticed it working now on devel.
> >>> However, I believe that is still not working for the release branch.
> >>>
> >>> Cheers,
> >>> Leo
> >>>
> >>> On Fri, Nov 20, 2015 at 3:37 PM, Jim Hester <james.f.hes...@gmail.com>
> wrote:
> >>>> The coverage tests were inadvertently not running, but they are now
> >>>> re-enabled.
> >>>>
> >>>> Please let us know if you notice any other problems
> >>>>
> >>>> Jim
> >>>>
> >>>> On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres <
> lcoll...@jhu.edu>
> >>>> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> In my packages I enabled testing (via testthat) a few weeks ago. I
> did
> >>>>> so as can be seen in
> >>>>>
> >>>>> https://github.com/leekgroup/derfinderHelper/commit/
> 26d9d5543d9082f85bbb2d0ae9f02c5c309b9a48
> >>>>> for the changes to tests/test-all.R You can see that the tests are
> >>>>> actually being run at
> >>>>>
> >>>>> http://bioconductor.org/checkResults/devel/bioc-
> LATEST/derfinderHelper/zin2-checksrc.html
> >>>>> Specifically at the lines:
> >>>>>
> >>>>> * checking tests ...
> >>>>>   Running ‘test-all.R’ [3s/13s]
> >>>>>  [3s/14s] OK
> >>>>>
> >>>>> I'm wondering if the coverage tests are only run at a less frequent
> >>>>> pace (say once per month) or if my tests/test-all.R file is still
> >>>>> posing problems to covr.
> >>>>>
> >>>>> Thanks,
> >>>>> Leo
> >>>>>
> >>>>> ___
> >>>>> Bioc-devel@r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>
>
>
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Re: [Bioc-devel] Availability shield URLs

[Leonardo Collado Torres]

Awesome, thanks Dan!

On Tue, Nov 8, 2016 at 9:40 AM, Martin Morgan <martin.mor...@roswellpark.org
> wrote:

> On 11/02/2016 11:54 AM, Leonardo Collado Torres wrote:
>
>> Hi,
>>
>> I'm just curious why
>> http://www.bioconductor.org/shields/availability/release/derfinder.svg
>> works but http://www.bioconductor.org/shields/availability/release/rec
>> ount.svg
>> doesn't (http://www.bioconductor.org/shields/availability/3.4/recount.svg
>> does work). The same is true for devel.
>>
>> derfinder has been around longer than recount, so that might be it. I
>> don't think that it's an alphabetical issue since
>> http://www.bioconductor.org/shields/availability/release/regionReport.svg
>> does work.
>>
>> This is a very minor thing. It's just easier to simply use
>> release/devel instead of 3.4/3.5 and changing it every cycle.
>>
>
> These are back to functioning now, thanks to some detective work from Dan.
> Thanks for the report. Martin
>
>
>> Best,
>> Leo
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

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Re: [Bioc-devel] Coverage test badge not updating

[Leonardo Collado Torres]

Hi,

I know that there are several old threads about the coverage badges
including this thread. Basically, while Bioc 3.4 was in devel, the
coverage badges didn't work for Bioc release (3.3). However, now that
3.4 has been released, the badges for Bioc-release (3.4) are still not
working and they only work for Bioc-devel (3.5).

In one of the threads, Dan mentioned that something at codecov had
changed and that he was going to ask for advice on how to proceed. I'm
just curious if there are any updates on this issue. If it's only
possible to have the coverage badges work for one branch, then it
might be best to leave them in Bioc-devel (given Jim's arguments
earlier) and remove them from Bioc-release.

Best,
Leo

On Mon, Nov 23, 2015 at 4:25 PM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
>
> Thank you for fixing this Jim! I noticed it working now on devel.
> However, I believe that is still not working for the release branch.
>
> Cheers,
> Leo
>
> On Fri, Nov 20, 2015 at 3:37 PM, Jim Hester <james.f.hes...@gmail.com> wrote:
> > The coverage tests were inadvertently not running, but they are now
> > re-enabled.
> >
> > Please let us know if you notice any other problems
> >
> > Jim
> >
> > On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres <lcoll...@jhu.edu>
> > wrote:
> >>
> >> Hi,
> >>
> >> In my packages I enabled testing (via testthat) a few weeks ago. I did
> >> so as can be seen in
> >>
> >> https://github.com/leekgroup/derfinderHelper/commit/26d9d5543d9082f85bbb2d0ae9f02c5c309b9a48
> >> for the changes to tests/test-all.R You can see that the tests are
> >> actually being run at
> >>
> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinderHelper/zin2-checksrc.html
> >> Specifically at the lines:
> >>
> >> * checking tests ...
> >>   Running ‘test-all.R’ [3s/13s]
> >>  [3s/14s] OK
> >>
> >> I'm wondering if the coverage tests are only run at a less frequent
> >> pace (say once per month) or if my tests/test-all.R file is still
> >> posing problems to covr.
> >>
> >> Thanks,
> >> Leo
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >

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Re: [Bioc-devel] github-mirror of ensembldb out of sync with BioC svn

[Leonardo Collado Torres]

Hi,

The same is true for recount and regionReport. derfinder and my other
packages are in sync though.

Best,
Leo

On Wed, Oct 19, 2016 at 3:34 AM, Rainer Johannes 
wrote:

> I just wanted to report that the github-mirror for ensembldb is out of
> sync with the BioC svn.
> You're most likely already working on that.
>
> In any rate, thanks for your great work!
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Re: [Bioc-devel] Merging two CharacterList objects doesn't work in Bioc-devel

[Leonardo Collado Torres]

Thanks Hervé for fixing this!

Best,
Leo

On Sat, Sep 10, 2016 at 5:47 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> Hi Leonardo,
>
> Not really intended. Should be addressed in S4Vectors 0.11.14.
>
> Cheers,
> H.
>
>
> On 09/08/2016 12:14 PM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> With Bioc-release I can run without problems the following code:
>>
>> library('GenomicRanges')
>> l <- CharacterList(list(NA, NA, '1', '2'))
>> r <- CharacterList(as.list(letters[1:4]))
>> tmp <- merge(l, r, all = TRUE)
>>
>> However, it gives an error with Bioc-devel:
>>
>> Error in V_recycle(value, x, x_what = "value", skeleton_what = "x") :
>>   'NROW(value)' is 0 but 'length(x)' is not
>> In addition: Warning messages:
>> 1: In if (any(duplicated(object))) warning(wmsg("Some of the objects
>> to merge contain ",  :
>>   the condition has length > 1 and only the first element will be used
>> 2: In if (any(duplicated(object))) warning(wmsg("Some of the objects
>> to merge contain ",  :
>>   the condition has length > 1 and only the first element will be used
>>
>>
>> Is this intended?
>>
>> Best,
>> Leo
>>
>>
>>
>> Bioc-release info:
>>
>>> library(GenomicRanges)
>>
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>>
>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>> clusterExport, clusterMap, parApply, parCapply, parLapply,
>> parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following objects are masked from ‘package:stats’:
>>
>> IQR, mad, xtabs
>>
>> The following objects are masked from ‘package:base’:
>>
>> anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>> duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
>> is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
>> paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
>> Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
>> unique, unsplit
>>
>> Loading required package: S4Vectors
>> Loading required package: stats4
>>
>> Attaching package: ‘S4Vectors’
>>
>> The following objects are masked from ‘package:base’:
>>
>> colMeans, colSums, expand.grid, rowMeans, rowSums
>>
>> Loading required package: IRanges
>> Loading required package: GenomeInfoDb
>>>
>>> l <- CharacterList(list(NA, NA, '1', '2'))
>>> r <- CharacterList(as.list(letters[1:4]))
>>> tmp <- merge(l, r, all = TRUE)
>>> tmp
>>
>>   group group_name value
>> 1 1a
>> 2 1 
>> 3 2b
>> 4 2 
>> 5 31
>> 6 3c
>> 7 42
>> 8 4d
>>>
>>> options(width = 120); devtools::session_info()
>>
>> Session info
>> ---
>>  setting  value
>>  version  R version 3.3.1 (2016-06-21)
>>  system   x86_64, darwin13.4.0
>>  ui   X11
>>  language (EN)
>>  collate  en_US.UTF-8
>>  tz   America/New_York
>>  date 2016-09-08
>>
>> Packages
>> ---
>>  package   * version date   source
>>  BiocGenerics  * 0.18.0  2016-05-04 Bioconductor
>>  colorout  * 1.1-2   2016-05-05 Github (jalvesaq/colorout@6538970)
>>  devtools1.12.0  2016-06-24 CRAN (R 3.3.0)
>>  digest  0.6.9   2016-01-08 CRAN (R 3.3.0)
>>  GenomeInfoDb  * 1.8.3   2016-07-13 Bioconductor
>>  GenomicRanges * 1.24.2  2016-06-15 Bioconductor
>>  IRanges   * 2.6.1   2016-06-19 Bioconductor
>>  memoise 1.0.0   2016-01-29 CRAN (R 3.3.0)
>>  S4Vectors * 0.10.2  2016-07-08 Bioconductor
>>  withr   1.0.2   2016-06-20 CRAN (R 3.3.0)
>>  XVector 0.12.0  2016-05-04 Bioconductor
>>  zlibbioc1.18.0  2016-05-04 Bioconductor
>>>
>>>
>>
>> Bioc-devel info:
>>
>>> library(GenomicRanges)
>>
>> Loading required package: stats4
>> Loading required package: BiocGenerics
>> Loading requir