Re: [Bioc-devel] Help with setting up a build environment to match

[Stephanie Gogarten]

I have found the BIocnductor docker images very helpful in reproducing the
build environment:
https://www.bioconductor.org/help/docker/

I used a combination of the examples under "modifying the images" to get a
version of the docker images that would build my vignettes, and also
install all dependencies needed to test my package. Then I mount the
directory that contains my package repository when starting up a docker
container:

docker run -it -v /Users/stephanie/Bioconductor:/home --user rstudio
bioconductor_docker_genesis:devel bash

That gives me a shell prompt in which I can run "R CMD build" and "R CMD
check". Since the docker container is viewing my local repository, I can
make changes and then re-run the checks.

best wishes,
Stephanie

On Fri, Apr 24, 2020 at 2:03 PM Andris Jankevics 
wrote:

> Hi,
>
>
> Are you using R 4.00 on Ubuntu?
>
> Travis error indicates that you are using class(), output of this command
> has changed.
>
>
> https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq
>
> BW,
> Andris
>
> On 24 Apr 2020 20:40, kone...@bcgsc.ca wrote:
> A package I maintain, contiBAIT, is failing to build on the BioC test
> servers.
>
>
>
> https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv
>
>
> It's also failing on my Travis build set up on GitHub
>
>
> https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114
>
>
> But I can't reproduce this in my local environment. R CMD build runs just
> fine against the source, with no errors. I'm even running Ubuntu 18.04.
>
>
>
> Can anyone suggest a relatively easy way to exactly reproduce the build
> environment on Travis or the BioC build servers so  I can reproduce this
> error and debug it?
>
>
> Thanks!
>
>
>
>
> [[alternative HTML version deleted]]
>
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>
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-- 

Stephanie M. Gogarten, PhD

Team Lead, Sample QC and Analysis Software / TOPMed Data Coordinating Center


Senior Research Scientist / Genetic Analysis Center


Department of Biostatistics 

UNIVERSITY OF WASHINGTON



UW Tower Box 359461

4333 Brooklyn Ave NE, Seattle, WA 98195

206.221.0757

sdmor...@uw.edu

she/her/hers

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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Hervé,

Thank you! You saved me.

Best!

Your sincerely,

Jianhong Ou

> On Apr 24, 2020, at 5:59 PM, Hervé Pagès  wrote:
> 
> Hi Jianhong,
> 
> I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good 
> news is that I no longer get a TIMEOUT with this new R:
> 
> machv2:meat biocbuild$ time R CMD build motifStack
> * checking for file ‘motifStack/DESCRIPTION’ ... OK
> * preparing ‘motifStack’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * building ‘motifStack_1.31.2.tar.gz’
> 
> 
> real1m33.576s
> user1m26.714s
> sys0m3.815s
> 
> So maybe it was a temporary issue with early Mac builds of R 4.0.
> 
> Please keep an eye on tomorrow's report (Saturday) and let me know if the 
> TIMEOUT is still there.
> 
> Thanks,
> H.
> 
> 
>> On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
>> Hi Herve,
>> Thank you for your help.
>> Jianhong.
>> On 4/17/20, 4:14 PM, "Hervé Pagès"  wrote:
>> For some reasons the generation of the plots in the vignette is VERY
>> slow on machv2. 'R CMD build' actually completed... after 6h! This is
>> still under investigation.
>>  Best,
>> H.
>>   On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
>> > Hi,
>> >
>> > I got timeout for my package motifStack in machv2. But I don't know 
>> what cuased the issue.
>> >
>> > Any help would be greatly appreciated.
>> >
>> > Jianhong.
>> > 
>> > From: Jianhong Ou, Ph.D.
>> > Sent: Wednesday, April 15, 2020 7:53 AM
>> > To: bioc-devel@r-project.org 
>> > Subject: Got timeout for machv2 BUILD
>> >
>> > Hi,
>> >
>> > Hope you are doing well.
>> >
>> > I got timeout for my package motifStack in machv2. The ellapsedTime is 
>> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 
>> seconds. I have limited information how to debug.
>> > Could you share your suggestion? Thank you.
>> >
>> >
>> >
>> > Yours Sincerely,
>> >
>> > Jianhong Ou
>> >
>> > Email: jianhong...@duke.edu
>> > Bioinformatician II
>> > Department of Cell Biology
>> > Duke University School of Medicine
>> > Durham, NC, 27710
>> >
>> > Confidentiality Notice:\ This e-mail message, including 
>> ...{{dropped:12}}
>> >
>> > ___
>> > 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=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w=
>> >
>>  --
>> 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
>> 
> 
> -- 
> 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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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Hervé Pagès]

LOL

On 4/24/20 15:00, Jianhong Ou, Ph.D. wrote:

Hi Hervé,

Thank you! You saved me.

Best!

Your sincerely,

Jianhong Ou


On Apr 24, 2020, at 5:59 PM, Hervé Pagès  wrote:

Hi Jianhong,

I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good 
news is that I no longer get a TIMEOUT with this new R:

machv2:meat biocbuild$ time R CMD build motifStack
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* preparing ‘motifStack’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘motifStack_1.31.2.tar.gz’


real1m33.576s
user1m26.714s
sys0m3.815s

So maybe it was a temporary issue with early Mac builds of R 4.0.

Please keep an eye on tomorrow's report (Saturday) and let me know if the 
TIMEOUT is still there.

Thanks,
H.



On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
Hi Herve,
Thank you for your help.
Jianhong.
On 4/17/20, 4:14 PM, "Hervé Pagès"  wrote:
 For some reasons the generation of the plots in the vignette is VERY
 slow on machv2. 'R CMD build' actually completed... after 6h! This is
 still under investigation.
  Best,
 H.
   On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
 > Hi,
 >
 > I got timeout for my package motifStack in machv2. But I don't know what 
cuased the issue.
 >
 > Any help would be greatly appreciated.
 >
 > Jianhong.
 > 
 > From: Jianhong Ou, Ph.D.
 > Sent: Wednesday, April 15, 2020 7:53 AM
 > To: bioc-devel@r-project.org 
 > Subject: Got timeout for machv2 BUILD
 >
 > Hi,
 >
 > Hope you are doing well.
 >
 > I got timeout for my package motifStack in machv2. The ellapsedTime is 
2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I 
have limited information how to debug.
 > Could you share your suggestion? Thank you.
 >
 >
 >
 > Yours Sincerely,
 >
 > Jianhong Ou
 >
 > Email: jianhong...@duke.edu
 > Bioinformatician II
 > Department of Cell Biology
 > Duke University School of Medicine
 > Durham, NC, 27710
 >
 > Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
 >
 > ___
 > 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=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w=
 >
  --
 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
 


--
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


--
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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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Hervé Pagès]

Hi Jianhong,

I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the 
good news is that I no longer get a TIMEOUT with this new R:


machv2:meat biocbuild$ time R CMD build motifStack
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* preparing ‘motifStack’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘motifStack_1.31.2.tar.gz’


real1m33.576s
user1m26.714s
sys 0m3.815s

So maybe it was a temporary issue with early Mac builds of R 4.0.

Please keep an eye on tomorrow's report (Saturday) and let me know if 
the TIMEOUT is still there.


Thanks,
H.


On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:

Hi Herve,

Thank you for your help.

Jianhong.

On 4/17/20, 4:14 PM, "Hervé Pagès"  wrote:

 For some reasons the generation of the plots in the vignette is VERY
 slow on machv2. 'R CMD build' actually completed... after 6h! This is
 still under investigation.
 
 Best,

 H.
 
 
 On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:

 > Hi,
 >
 > I got timeout for my package motifStack in machv2. But I don't know what 
cuased the issue.
 >
 > Any help would be greatly appreciated.
 >
 > Jianhong.
 > 
 > From: Jianhong Ou, Ph.D.
 > Sent: Wednesday, April 15, 2020 7:53 AM
 > To: bioc-devel@r-project.org 
 > Subject: Got timeout for machv2 BUILD
 >
 > Hi,
 >
 > Hope you are doing well.
 >
 > I got timeout for my package motifStack in machv2. The ellapsedTime is 
2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I 
have limited information how to debug.
 > Could you share your suggestion? Thank you.
 >
 >
 >
 > Yours Sincerely,
 >
 > Jianhong Ou
 >
 > Email: jianhong...@duke.edu
 > Bioinformatician II
 > Department of Cell Biology
 > Duke University School of Medicine
 > Durham, NC, 27710
 >
 > Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
 >
 > ___
 > 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=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w=
 >
 
 --

 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
 



--
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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Re: [Bioc-devel] Help with setting up a build environment to match

[Andris Jankevics]

Hi,


Are you using R 4.00 on Ubuntu?

Travis error indicates that you are using class(), output of this command has 
changed.

https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq

BW,
Andris

On 24 Apr 2020 20:40, kone...@bcgsc.ca wrote:
A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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Re: [Bioc-devel] Help with setting up a build environment to match

[Fan, Jean]

Hi Kieran,

It looks like your Travis build is failing because of your vignettes:

Error: processing vignette 'contiBAIT.Rnw' failed with diagnostics:
6542 chunk 13 (label = orderAllLinkageGroupsExampleb)
6543Error in if (spearmanCor < 0) { : missing value where TRUE/FALSE needed
6544
6545





The BioC Test servers point to the same vignette issue.

Your R CMD build runs may have --no-build-vignettes or --no-vignettes by 
default.

Best,
Jean

On Apr 24, 2020, at 3:11 PM, Kieran O'Neill 
mailto:kone...@bcgsc.ca>> wrote:

A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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[Bioc-devel] Help with setting up a build environment to match

[Kieran O'Neill]

A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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[Bioc-devel] Bioconductor annotation packages delay

[Interdonato, Kayla]

Hello Bioconductor community,

There have been some recent changes to our workflow for creating the GO.db
annotation package. The information was previously provided in SQL file format,
but these files are no longer updated and obo files are created instead.
Accounting for this change has caused a delay in releasing the next version of
GO.db, which in turn affects the Org and TxDb packages. Instead of making the
new versions available over the weekend and potentially causing issues for
packages that depend on them, we have decided to release the next versions of
the GO.db, Org, and TxDb shortly after our Bioc 3.11 release next week. This
will allow for maintainers to make any necessary changes to their packages
without concern of making the cutoff for the release. We will announce here and
on the support site when these new versions are available.

Thank you for your patience.

Kayla E. Interdonato, MS
Programmer/Analyst
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
(716)845-1300 x4621


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] 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

[Gavin Lloyd]

I also had an issue related to cropping using BiocStyle pdf_document, and used 
the same fix.
https://github.com/Bioconductor/BiocStyle/issues/75
Gavin

From: Bioc-devel  on behalf of 
mtmorgan.b...@gmail.com 
Sent: 24 April 2020 11:26:30
To: Leonardo Collado Torres; Bioc-devel
Cc: Andrzej Oleś
Subject: Re: [Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the 
Bioc 3.11 Linux builder

Thanks for the detective work Leo; to me it sounds like, for robust output 
(function more important than form) BiocStyle should not try to crop images.

Martin

On 4/24/20, 12:52 AM, "Bioc-devel on behalf of Leonardo Collado Torres" 
 wrote:

Hi Bioc-devel again,


I believe that I have found the source of my regionReport problem and
a workaround. We'll know tomorrow if it goes through the Bioc builds
but it works at
https://github.com/leekgroup/regionReport/actions/runs/86364716.

The problem is related to
https://github.com/ropensci/magick/issues/171 and similar issues. The
workaround is to use `crop = NULL` on R Markdown code chunks to
disable the default image cropping behavior by
BiocStyle::html_document, and thus avoid cache issues from magick (R)
and ImageMagick (not R).

Both the Bioc-devel Linux machine and GitHub Actions using
Bioconductor devel run into a problem where there's not enough
resources in the cache for cropping the images produced by
regionReport::derfinderReport(). Either (a) the Bioc-devel Windows and
macOS machines don't have magick installed (so no cropping gets
attempted), (b) use a compiled version of magick that ships with the
right version of ImageMagick, or (c) they have more resources than the
bioc Linux build machine and the bioc devel docker running on GHA
Linux

In any case, disabling cropping circumvents this issue.


Here's the full investigative report.




## A new lead

I recently stumbled upon [1] and re-reading it now I see that they
link to [2] which mentions that BiocStyle crops by default and that
this can be turned off using `crop = NULL`.

regionReport uses BiocStyle::html_document both for its vignettes as
well as the reports it makes by default. Actually at [3], which was
built using the Bioconductor devel docker & GitHub Actions (GHA), I
see tons of messages that are similar to:

## The magick package is required to crop
"basicExploration_files/figure-html/pvals-1.png" but not available.

For reference, [4] is how that example from
regionReport::derfinderReport() looks built using GHA. I copied the
log of messages to a gist at [5]. From [6] I found [7] where Mike
Smith explains to Aaron Lun the default behavior of BiocStyle and
again suggests to use `crop = NULL` just like Yihui Xie mentioned
earlier at [2]. I see at [8] that Kevin Rue-Albrecht also ran into a
`crop = NULL` problem in iSEE.


So I have a good lead now!


## Adding magick to Suggests

We can see clearly that magick is not available on my GitHub Actions
run using the Biocondutor devel docker: regionReport 1.21.7 doesn't
mention magick on it's DESCRIPTION so it's never installed on GHA.
However, magick is likely installed on the Bioconductor 3.11 Linux
build machine and thus it is used for cropping. At [9] I bumped
regionReport to 1.21.8 after adding magick to suggests. Actually, this
is what Yihui Xie recommends BiocStyle could/should do in [2]. That
crashed and burned on GHA Linux with Bioc-docker at [10], thus
reproducing the Linux build machine error.

Quitting from lines 224-229 (basicExploration.Rmd)
35Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
36R: cache resources exhausted

`/tmp/RtmpfaoqUE/Rbuild74c3a6bf655/regionReport/vignettes/report/html/basicExploration_files/figure-html/plotRegions-17.png'
@ error/cache.c/OpenPixelCache/4083

Actually, this error message is more informative than the one from the
Bioc Linux builder as it gives the actual image name where it all
burned down.


## Moving problematic code from the vignette to an example

At [11] I moved the problematic code to an example instead of the
vignette. On GHA, it failed again at [12] predictably on another image
than in [10]. Also predictably, R CMD build worked this time, but R
CMD check failed. However, now the I get the full logs that help me
see the details much better and link it to code [13] (so if that was
the bug source, I would know where to look).

Quitting from lines 399-400 (basicExploration.Rmd)
355Error in magick_image_trim(image, fuzz) :
356 R: cache resources exhausted

`/__w/regionReport/regionReport/check/regionReport.Rcheck/derfinderReport-example/basicExploration/basicExploration_files/figure-html/genomeOverview3-1.png'
@ error/cache.c/OpenPixelCache/4083
357Calls: 

Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

[Stian Lågstad]

Thank you very much for the help so far!

On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès  wrote:

> OK, thanks testing that. This suggests that the problem is on our
> side... sigh! I will need to dig deeper into this.
>
> Best,
> H.
>
>
> On 4/23/20 22:57, Bemis, Kylie wrote:
> > Worked for me without errors or warnings:
> >
> > kuwisdelu@Eva-02-Dash Projects % R CMD build chimeraviz
> > * checking for file ‘chimeraviz/DESCRIPTION’ ... OK
> > * preparing ‘chimeraviz’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... OK
> > * checking for LF line-endings in source and make files and shell scripts
> > * checking for empty or unneeded directories
> > Removed empty directory ‘chimeraviz/docker’
> > * building ‘chimeraviz_1.13.8.tar.gz’
> >
> > kuwisdelu@Eva-02-Dash Projects % R CMD INSTALL chimeraviz_1.13.8.tar.gz
> > * installing to library ‘/Users/kuwisdelu/Library/R/4.0/library’
> > * installing *source* package ‘chimeraviz’ ...
> > ** using staged installation
> > ** R
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded from temporary location
> > ** testing if installed package can be loaded from final location
> > ** testing if installed package keeps a record of temporary installation
> > path
> > * DONE (chimeraviz)
> >
> > Under:
> >
> >> sessionInfo()
> > R version 4.0.0 RC (2020-04-18 r78249)
> > Platform: x86_64-apple-darwin17.0 (64-bit)
> > Running under: macOS Catalina 10.15.3
> >
> > Matrix products: default
> > BLAS:
> > /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> > LAPACK:
> >
> /Library/Frameworks/R.framework/Versions/4.0/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_4.0.0 tools_4.0.0
> >
> > The vignette looks okay as far as I can tell.
> >
> > -Kylie
> >
> >
> >
> >
> >
> >
> >> On Apr 24, 2020, at 1:40 AM, Hervé Pagès  >> > wrote:
> >>
> >> Interesting indeed. Thanks for checking this.
> >>
> >> Even though I'm not sure what conclusion to draw from all this.
> >>
> >> Since you are on a Mac, can I ask you another big favor? Do you think
> >> you could run 'R CMD build' on chimeraviz and see if you can reproduce
> >> the error we see on the build report here:
> >>
> >>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fchimeraviz%2Fmachv2-buildsrc.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0
> >> <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fbioconductor.org-252FcheckResults-252F3.11-252Fbioc-2DLATEST-252Fchimeraviz-252Fmachv2-2Dbuildsrc.html-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3Ds9fJRfwSMO0UkPEwdmrW7mZhEM-252FgCOYtQm3HO12DknA-253D-26amp-3Breserved-3D0=DwMGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ChvNTQebsUvVKYAGSEtFgFNOcwgSzxXYjQ69oO9oBM0=Rkoe-LwrUsVZyqv9zyv00KH__7fWXhf-n8-ZTmYFdP4=
> >
> >>
> >> Get the source with
> >>
> >>  git clone
> >>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeravizdata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3Dreserved=0
> >>
> >> Thanks,
> >> H.
> >>
> >>
> >> On 4/23/20 21:55, Bemis, Kylie wrote:
> >>> That’s interesting. I did:
>  BiocManager::install("Cardinal", type="mac.binary.el-capitan”)
>  browseVignettes("Cardinal")
> >>> from R 3.6.3, and the figures using transparency in the vignettes
> >>> look fine to me.
> >>> When I use X11() to reproduce the warning locally, the transparent
> >>> colors get truncated, so that the higher-alpha colors appear opaque
> >>> and the lower-alpha colors don’t appear at all.
> >>> However, in the merida1 vignette, the figures appear as I’d normally
> >>> get form quartz() or pdf() locally, which don’t produce warnings for
> >>> me on macOS 10.15.3.
> >>> -Kylie
>  On Apr 24, 2020, at 12:39 AM, Hervé Pagès   > wrote:
> 
>  Hi Kylie,
> 
>  I get the warnings on merida1 for Cardinal too e.g. when I run the
>  code in the 

Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

[Hervé Pagès]

OK, thanks testing that. This suggests that the problem is on our 
side... sigh! I will need to dig deeper into this.


Best,
H.


On 4/23/20 22:57, Bemis, Kylie wrote:

Worked for me without errors or warnings:

kuwisdelu@Eva-02-Dash Projects % R CMD build chimeraviz
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* preparing ‘chimeraviz’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘chimeraviz/docker’
* building ‘chimeraviz_1.13.8.tar.gz’

kuwisdelu@Eva-02-Dash Projects % R CMD INSTALL chimeraviz_1.13.8.tar.gz
* installing to library ‘/Users/kuwisdelu/Library/R/4.0/library’
* installing *source* package ‘chimeraviz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation 
path

* DONE (chimeraviz)

Under:


sessionInfo()

R version 4.0.0 RC (2020-04-18 r78249)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/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_4.0.0 tools_4.0.0

The vignette looks okay as far as I can tell.

-Kylie






On Apr 24, 2020, at 1:40 AM, Hervé Pagès > wrote:


Interesting indeed. Thanks for checking this.

Even though I'm not sure what conclusion to draw from all this.

Since you are on a Mac, can I ask you another big favor? Do you think 
you could run 'R CMD build' on chimeraviz and see if you can reproduce 
the error we see on the build report here:


https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fchimeraviz%2Fmachv2-buildsrc.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0 



Get the source with

 git clone 
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeravizdata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3Dreserved=0


Thanks,
H.


On 4/23/20 21:55, Bemis, Kylie wrote:

That’s interesting. I did:

BiocManager::install("Cardinal", type="mac.binary.el-capitan”)
browseVignettes("Cardinal")
from R 3.6.3, and the figures using transparency in the vignettes 
look fine to me.
When I use X11() to reproduce the warning locally, the transparent 
colors get truncated, so that the higher-alpha colors appear opaque 
and the lower-alpha colors don’t appear at all.
However, in the merida1 vignette, the figures appear as I’d normally 
get form quartz() or pdf() locally, which don’t produce warnings for 
me on macOS 10.15.3.

-Kylie
On Apr 24, 2020, at 12:39 AM, Hervé Pagès > wrote:


Hi Kylie,

I get the warnings on merida1 for Cardinal too e.g. when I run the 
code in the Cardinal-2-stats vignette:


   merida1:vignettes biocbuild$ pwd
   /Users/biocbuild/bbs-3.10-bioc/meat/Cardinal/vignettes

   merida1:vignettes biocbuild$ R CMD Stangle Cardinal-2-stats.Rmd
   Output file:  Cardinal-2-stats.R

   merida1:vignettes biocbuild$ R
   ...
   > source("Cardinal-2-stats.R", echo=TRUE)
   ...
   There were 14 warnings (use warnings() to see them)
   > warnings()
   Warning messages:
   1: In rect(left, top, r, b, angle = angle, density = density,  ... :
 semi-transparency is not supported on this device: reported 
only once