Re: [R-pkg-devel] Unable to get past CRAN submission checks for package cubature

[Dirk Eddelbuettel]

On 10 May 2021 at 13:01, Balasubramanian Narasimhan wrote:
| It appears that I am unable to get beyond the auto-check service. Any 
| suggestions?

I have tried for several weeks, and four emails, to get an answer concerning
an auto-archived submission. Ironically, it aimed to address the very 'error
on one platform' issue over which it was archived.

I still haven't heard back.

Dirk

-- 
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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[R-pkg-devel] Unable to get past CRAN submission checks for package cubature

[Balasubramanian Narasimhan]

I submitted a minor update of cubature (suggesting rmarkdown for 
vignettes) and received a message that the package generated warnings. 
However, the warnings were noted to be untrustworthy (see email below). 
I noted this in the submission comments as well as the reply to the 
auto-check email.

It appears that I am unable to get beyond the auto-check service. Any 
suggestions?

-Naras

 Forwarded Message 

Subject:Re: [CRAN-pretest-archived] CRAN submission cubature 2.0.4.2
Date:   Thu, 6 May 2021 12:51:37 -0700
From:   Balasubramanian Narasimhan 
To: cran-submissi...@r-project.org, na...@stat.stanford.edu



Dear CRAN,

As explained in my submission comment, the warning is noted to be flaky 
in the message below.

Thank you.

-Naras

On 18/03/2021 13:05, Kurt Hornik wrote:

>> Uwe Ligges writes:
>
>> Dear Naras,
>> your package cubature shows compiler warnings under Windows:
>> 
>
>> Any chance getting rid of these? Please try and resubmit.
>
> Interestingly, r-release-macos shows this too ...

I think -Warray-bounds is known to be flaky in earlier compilers.  I do 
not see this on macOS with Apple Clang 11.5 (latest for High Sierra) or 
12.4 (current) and nor does Tomas for GCC 10 on Windows.


-- 
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
On 5/6/21 12:27 PM, lig...@statistik.tu-dortmund.de wrote:
> Dear maintainer,
>   
> package cubature_2.0.4.2.tar.gz does not pass the incoming checks 
> automatically, please see the following pre-tests:
> Windows:
> Status: 1 WARNING
> Debian:
> Status: OK
>   
> Last released version's CRAN status: WARN: 3, NOTE: 10
> See:
>   
> CRAN Web:
>   
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on the 
> R-package-devel mailing list:
> 
> If you are fairly certain the rejection is a false positive, please reply-all 
> to this message and explain.
>   
> More details are given in the directory:
> 
> The files will be removed after roughly 7 days.
>   
> *** Strong rev. depends ***: ALTopt apTreeshape bivquant BNSP calibrator 
> clusteredinterference coga cold dbmss DRAYL dvmisc ei equivalenceTest 
> fMultivar GAS GB2 GPCMlasso GRCdata highfrequency hyper2 ICAOD inctools 
> MCMCglmm MIRES MMDCopula MWright NonNorMvtDist np OBASpatial ODS optimStrat 
> PCMRS planar pooling Power2Stage PowerTOST ProFit QGglmm robustlmm skedastic 
> SphericalCubature spNetwork statsr SurvDisc symmoments TCIU tseriesEntropy 
> UPCM vines WLinfer yuima
>   
> Best regards,
> CRAN teams' auto-check service
>
> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
> Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
>Maintainer: 'Balasubramanian Narasimhan'
>
> Flavor: r-devel-windows-ix86+x86_64
> Check: whether package can be installed, Result: WARNING
>Found the following significant warnings:
>  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between 
> offset 0 and size [4294967292, 2147483647] [-Warray-bounds]
>  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between 
> offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
>See 'd:/RCompile/CRANincoming/R-devel/cubature.Rcheck/00install.out' for 
> details.

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Re: [Bioc-devel] CTCF AnnotationHub package

[Kern, Lori]

The issue was immediately closed because of the issue with the version number 
as indicated directly on the message in the issue.

https://github.com/Bioconductor/Contributions/issues/2108#issuecomment-836766063


As far as uploading data to S3,  As indicated in the documentation
http://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/CreateAHubPackage.html#uploading-data-to-s3

You will need credentials.  I will respond in a separate, off-list email with 
the appropriate credentials.

Cheers,




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 Mikhail 
Dozmorov 
Sent: Monday, May 10, 2021 10:27 AM
To: bioc-devel 
Subject: [Bioc-devel] CTCF AnnotationHub package

I'm submitting the CTCF AnnotationHub package,
https://secure-web.cisco.com/1MNl9vTKVa0ZlGBJL-piC_7GO01l7GgpYIByAUlM3i7JMVk42R4bU2gi3DXZFmPHTNlVdA2gZlQAzJ3zf1igx1dbFP3HqWUFKa53s-e8hlHtJZdd88OEV0N0tLFeCm6qcIbMMmyYraXykAKK6Voh6ZiICt-aX1z1IvIcPlgJkkMmK1FsxDuCMLVqZpb-MWv17wXJcZZwRnEbMuTvHUX7AgzjRiDjqURufOHIxzHnJxTNZAXQLIB9Q4LT99Mn0EtfgPeb9YottC7W3WcqllZDlRLLvov23uzd9EcoIyiIjDec4xFnopmDXhAsqamQ11I-syfktWxXQ-hewCA32iB9emw/https%3A%2F%2Fgithub.com%2Fmdozmorov%2FCTCF,
 with the coordinates of predicted CTCF
binding sites as GRanges. The package builds on all OSs, passes
AnnotationHubData:::makeAnnotationHubMetadata(). It has been submitted to
the tracker, but was immediately closed
https://secure-web.cisco.com/1wm5ko3vx1pHP8AvTnFcYoIJuake2JihUpGToJTa__vkHn0g6Vg6gE38DsixxXzTp3wOc_r5FaInXHvK7LX4_l8oFX3F4CbuIG9vBRR-uIIkTPUXc8kuFHT2yZ-2XgtxlI0jVwg0DOXOpjeUnGu1CuLclL5ly-mcNXJk-4GoSjQGPOG8tMEVp6TeOe4yVta4Dsd7JyJcC8fzV6NjVvB4eEBy9h9d3yntoc_crF7OCQkdrlY0Mc1iECBU8CoxzmKrVdXIkB0-aHW4N2cB4sFbm0_da-vG3xnTZPlDaA5HCzkLAkdqIc1ukUoDmpLMbCFj7fl98friiY-crxrLbJzGNJw/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2108
 Please, advise
what to do next and how to upload the data to AWS S3?

Thanks,
Mikhail

---
Mikhail Dozmorov, Ph.D.
Department of Biostatistics, VCU
E-mail:  mdozmo...@vcu.edu

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[Bioc-devel] CTCF AnnotationHub package

[Mikhail Dozmorov]

I'm submitting the CTCF AnnotationHub package,
https://github.com/mdozmorov/CTCF, with the coordinates of predicted CTCF
binding sites as GRanges. The package builds on all OSs, passes
AnnotationHubData:::makeAnnotationHubMetadata(). It has been submitted to
the tracker, but was immediately closed
https://github.com/Bioconductor/Contributions/issues/2108. Please, advise
what to do next and how to upload the data to AWS S3?

Thanks,
Mikhail

---
Mikhail Dozmorov, Ph.D.
Department of Biostatistics, VCU
E-mail:  mdozmo...@vcu.edu

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Re: [Bioc-devel] Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check

[Kern, Lori]

Please also remember to update package NEWS files for any information about 
changes to your packages during this last development cycle.  Bioconductor 
collates all package news files as part of the release announcement.  See the 
example from the 3.12 release announcement here: 
http://bioconductor.org/news/bioc_3_12_release/

Cheers,


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 Kern, Lori 

Sent: Monday, May 10, 2021 10:06 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioc 3.13 Feature Freeze and Deadline for passing R CMD 
build/check

Developers,

The release of Bioconductor 3.13 is scheduled for next week. Please respect the 
'feature freeze' of 3.13 where we ask that all commits are limited to bug fixes 
and documentation (no more API changes).  The deadline to pass R CMD build and 
check on the daily builders is this coming Friday May 14th.  While you will be 
able to commit to the devel branch for release 3.13 up to the code freeze next 
Wednsday May 19th, commits by Friday ensure proper checking and propagation on 
the build system and accurate reflections of code changes on the build report 
and landing pages.

Thank you for your cooperation.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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] Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check

[Kern, Lori]

Developers,

The release of Bioconductor 3.13 is scheduled for next week. Please respect the 
'feature freeze' of 3.13 where we ask that all commits are limited to bug fixes 
and documentation (no more API changes).  The deadline to pass R CMD build and 
check on the daily builders is this coming Friday May 14th.  While you will be 
able to commit to the devel branch for release 3.13 up to the code freeze next 
Wednsday May 19th, commits by Friday ensure proper checking and propagation on 
the build system and accurate reflections of code changes on the build report 
and landing pages.

Thank you for your cooperation.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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 
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[Bioc-devel] BFG clean-up and reset for compartmap

[Johnson, Ben]

Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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Re: [Rd] R-devel new warning: no longer be an S4 object

[Martin Maechler]

> Jan Gorecki 
> on Mon, 10 May 2021 12:42:09 +0200 writes:

> Hi R-devs,
> R 4.0.5 gives no warning. Is it expected? Searching the news for "I("
> doesn't give any info. Thanks

> z = I(getClass("MethodDefinition"))

Now what exactly did you intend with the above line ?

I'm bold and say (for the moment) that the above line has always
been very dubious if not misleading,
and this "fact" is now finally revealed by the warning

> Warning message:
> In `class<-`(x, unique.default(c("AsIs", oldClass(x :
> Setting class(x) to multiple strings ("AsIs", "classRepresentation",
> ...); result will no longer be an S4 object

So, yes, the change has been on purpose to warn about problems,
you'd get later when trying to work with 'z'.


> [[alternative HTML version deleted]]

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Re: [Bioc-devel] Maintainer change Bioconductor packages

[Pablo Moreno]

Dear Nitesh,

I think that in the rush of Suhaib leaving, we didn’t finalise this process.

Is it acceptable to have a group email/account as maintainer? We would have 
gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team 
members. Then we wouldn’t need to repeat the process if any of us leaves.

Thanks,
Pablo

> On 28 Jan 2021, at 18:27, Nitesh Turaga  wrote:
> 
> Hi Suhaib,
> 
> You are correct, the maintainer needs to be changed if you are unable to 
> maintain the package further. You need to nominate another maintainer for the 
> packages you listed. 
> 
> Once the new maintainer steps in, 
> 
> 1. Change the Maintainer or Authors@R field in the DESCRIPTION file of the 
> package to reflect the change. 
> 
> 2. Maintainer has to have a BiocCredentials account. 
> 
> 3. Maintainer has to be subscripted to bioc-devel@r-project.org mailing list. 
> 
> Best,
> 
> Nitesh 
> 
> 
> On 1/28/21, 7:00 AM, "Suhaib Mohammed"  wrote:
> 
>To whom ever it may concern,
> 
>I have been maintaining the Bioconductor R packages (ExpressionAtlas and 
>ArrayExpress) of Gene Expression Atlas team at the EMBL-EBI. As I will 
>be leaving EBI, I understand the maintainer needs to be changed. Could 
>you point to the procedure for changing the maintainer ?
> 
>Expression Atlas - 
>https://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
>Array Express - 
>https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
> 
>Many thanks,
>Suhaib
> 
>-- 
>Suhaib Mohammed, Ph.D.
>Senior Bioinformatician
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton, Cambridge CB10 1SD
>United Kingdom
>tel : +44-1223494296
>email: suh...@ebi.ac.uk
> 

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Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

[Zhang, Bing]

Sorry, I used the wrong email address for the new maintainer. Here is the 
correct information:
First Name: Zhiao
Last Name: Shi
Email: zhiao@gmail.com

Bing

From: "Zhang, Bing" 
Date: Sunday, May 9, 2021 at 10:04 PM
To: "maintai...@bioconductor.org" , 
"bioc-devel@r-project.org" 
Cc: "justin@gmail.com" 
Subject: Transfer Maintainership of the Package NetSAM

Dear Sir or Madam,

I am the maintainer of the Bioconductor package NetSAM 
(https://bioconductor.org/packages/release/bioc/html/NetSAM.html ). My lab 
moved from the Vanderbilt University to the Baylor College of Medicine a few 
years ago, and my email address used for NetSAM was my Vanderbilt email account.

I would like to transfer the maintainership of NetSAM to a Lead Programer in my 
lab (cc’ed), please find below his contact information:
First Name: Zhiao
Last Name: Shi
Email: justin@gmail.com

Please let us know if you need additional information to make the transfer. 
Thanks!

Best regards,

Bing


Bing Zhang, Ph.D.
Professor of Molecular and Human Genetics
Breast Center
McNair Medical Institute Scholar
Cancer Prevention Research Institute of Texas (CPRIT) Scholar
Baylor College of Medicine
Houston, Texas 77030
Tel: 713-798-1443
Email: bing.zh...@bcm.edu
URL: http://www.zhang-lab.org

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[Bioc-devel] Transfer Maintainership of the Package NetSAM

[Zhang, Bing]

Dear Sir or Madam,

I am the maintainer of the Bioconductor package NetSAM 
(https://bioconductor.org/packages/release/bioc/html/NetSAM.html ). My lab 
moved from the Vanderbilt University to the Baylor College of Medicine a few 
years ago, and my email address used for NetSAM was my Vanderbilt email account.

I would like to transfer the maintainership of NetSAM to a Lead Programer in my 
lab (cc’ed), please find below his contact information:
First Name: Zhiao
Last Name: Shi
Email: justin@gmail.com

Please let us know if you need additional information to make the transfer. 
Thanks!

Best regards,

Bing


Bing Zhang, Ph.D.
Professor of Molecular and Human Genetics
Breast Center
McNair Medical Institute Scholar
Cancer Prevention Research Institute of Texas (CPRIT) Scholar
Baylor College of Medicine
Houston, Texas 77030
Tel: 713-798-1443
Email: bing.zh...@bcm.edu
URL: http://www.zhang-lab.org

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[Rd] R-devel new warning: no longer be an S4 object

[Jan Gorecki]

Hi R-devs,
R 4.0.5 gives no warning. Is it expected? Searching the news for "I("
doesn't give any info. Thanks

z = I(getClass("MethodDefinition"))
Warning message:
In `class<-`(x, unique.default(c("AsIs", oldClass(x :
  Setting class(x) to multiple strings ("AsIs", "classRepresentation",
...); result will no longer be an S4 object

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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Martin Morgan]

The data/experiment and many data/annotation packages are not hosted in our git 
(!) so it would be necessary to take another approach (rsync + untar?) to 
obtaining their source.

Martin

On 5/10/21, 6:03 AM, "Bioc-devel on behalf of Mike Smith" 
 wrote:

Hi Steffen,

Thanks for the feedback.  I've been referencing this email thread when
presenting about developing the code website, so it might be old but it
wasn't forgotten!

Right now I think we still don't quite meet your use case, as
https://code.bioconductor.org/ currently only lists the software packages,
so msdata can't actually be found there.  That choice was because I had
limited disk-space in my prototypes of the site and so didn't try copying
any other type of package, but it doesn't have to remain that way.  I don't
know how much space might be needed for the other types of package, and
it's something I'm happy to consider for the future.

Cheers,
Mike

On Mon, 10 May 2021 at 09:10, Neumann, Steffen 
wrote:

> Hi,
>
> this is a follow-up to a rather old thread, but with
> Mike Smith's (twitter: @grimbough)
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> > On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > > So, what if there was a MetaBioconductor site and repo similar to
> > > the
> > > MetaCRAN project? https://www.r-pkg.org/about
> > >
> > > Not sure exactly who maintains it (probably someone at RStudio),
> > > but it
> > > is largely automatic I believe, and it provides a full GitHub
> > > archive of
> > > *all* the packages on CRAN, which if this were done for
> > > Bioconductor
> > > would satisfy what I think Steffen is looking for, as well as lots
> > > of
> > > other advantages.
> > >
> > > It also has the advantage that it looks like 90% of the work would
> > > be
> > > done for Bioconductor with likely very little work required for
> > > the
> > > Bioconductor Admins (ideally 100% of work would be done for them).
> >
> > there has been some discussion of that, e.g.,
> >
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> >
> > but we will not do it (maintain a github mirror), for instance
> > because
> > some experiment data packages have commits that would require lfs,
> > because of issues with reliably  syncing data, and because of
> > confusion
> > it introduces on the 'official' repository.
> >
> > We do intend to provide a browsable interface to the official
> > git.bioconductor.org that would allow Steffen's use case during the
> > present release cycle; it is not currently available.
> >
> > A different solution would be to update the relevant ExperimentData
> > package to use ExperimentHub (see, e.g.,
> > https://github.com/LTLA/TENxBrainData for a relatively simple
> > example,
> > though not yet in Bioconductor) and the resource would then be
> > available
> > at a URL https://annotationhub.bioconductor.org/fetch/...
> >
> > Martin
> >
> > > Just a thought.
> > >
> > > -Robert
> > >
> > > Robert M Flight, PhD
> > > Bioinformatics Research Associate
> > > Puller of Rabbits from Hats
> > > Research Parasite
> > > Resource Center for Stable Isotope Resolved Metabolomics
> > > Manager, Systems Biology and Omics Integration Journal Club
> > > Markey Cancer Center
> > > CC434 Roach Building
> > > University of Kentucky
> > > Lexington, KY
> > >
> > > Twitter: @rmflight
> > > Web: rmflight.github.io 
> > > ORCID: http://orcid.org/-0001-8141-7788
> > > EM rfligh...@gmail.com 
> > > PH 502-509-1827 
> > >
> > > To call in the statistician after the experiment is done may be no
> > > more
> > > than asking him to perform a post-mortem examination: he may be
> > > able to
> > > say what the experiment died of. - Ronald Fisher
> > >
> > > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan
> > >  > > martin.mor...@roswellpark.org>>
> > > wrote:
> > >
> > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > >  > Hi,
> > >  >
> > >  > thanks for the answer, unfortunately
> > >  > not exactly what I meant. To be more precise:
> > >  >
> > >  > I want to point Galaxy to download (test) MS data files
> > >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> > >  >
> > >  > For that I need an ftp/http/https link to the files,
> > >  > and I was able to use
> > >  >
> 

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Mike Smith]

Hi Steffen,

Thanks for the feedback.  I've been referencing this email thread when
presenting about developing the code website, so it might be old but it
wasn't forgotten!

Right now I think we still don't quite meet your use case, as
https://code.bioconductor.org/ currently only lists the software packages,
so msdata can't actually be found there.  That choice was because I had
limited disk-space in my prototypes of the site and so didn't try copying
any other type of package, but it doesn't have to remain that way.  I don't
know how much space might be needed for the other types of package, and
it's something I'm happy to consider for the future.

Cheers,
Mike

On Mon, 10 May 2021 at 09:10, Neumann, Steffen 
wrote:

> Hi,
>
> this is a follow-up to a rather old thread, but with
> Mike Smith's (twitter: @grimbough)
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> > On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > > So, what if there was a MetaBioconductor site and repo similar to
> > > the
> > > MetaCRAN project? https://www.r-pkg.org/about
> > >
> > > Not sure exactly who maintains it (probably someone at RStudio),
> > > but it
> > > is largely automatic I believe, and it provides a full GitHub
> > > archive of
> > > *all* the packages on CRAN, which if this were done for
> > > Bioconductor
> > > would satisfy what I think Steffen is looking for, as well as lots
> > > of
> > > other advantages.
> > >
> > > It also has the advantage that it looks like 90% of the work would
> > > be
> > > done for Bioconductor with likely very little work required for
> > > the
> > > Bioconductor Admins (ideally 100% of work would be done for them).
> >
> > there has been some discussion of that, e.g.,
> >
> >
> > https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> >
> > but we will not do it (maintain a github mirror), for instance
> > because
> > some experiment data packages have commits that would require lfs,
> > because of issues with reliably  syncing data, and because of
> > confusion
> > it introduces on the 'official' repository.
> >
> > We do intend to provide a browsable interface to the official
> > git.bioconductor.org that would allow Steffen's use case during the
> > present release cycle; it is not currently available.
> >
> > A different solution would be to update the relevant ExperimentData
> > package to use ExperimentHub (see, e.g.,
> > https://github.com/LTLA/TENxBrainData for a relatively simple
> > example,
> > though not yet in Bioconductor) and the resource would then be
> > available
> > at a URL https://annotationhub.bioconductor.org/fetch/...
> >
> > Martin
> >
> > > Just a thought.
> > >
> > > -Robert
> > >
> > > Robert M Flight, PhD
> > > Bioinformatics Research Associate
> > > Puller of Rabbits from Hats
> > > Research Parasite
> > > Resource Center for Stable Isotope Resolved Metabolomics
> > > Manager, Systems Biology and Omics Integration Journal Club
> > > Markey Cancer Center
> > > CC434 Roach Building
> > > University of Kentucky
> > > Lexington, KY
> > >
> > > Twitter: @rmflight
> > > Web: rmflight.github.io 
> > > ORCID: http://orcid.org/-0001-8141-7788
> > > EM rfligh...@gmail.com 
> > > PH 502-509-1827 
> > >
> > > To call in the statistician after the experiment is done may be no
> > > more
> > > than asking him to perform a post-mortem examination: he may be
> > > able to
> > > say what the experiment died of. - Ronald Fisher
> > >
> > > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan
> > >  > > martin.mor...@roswellpark.org>>
> > > wrote:
> > >
> > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> > >  > Hi,
> > >  >
> > >  > thanks for the answer, unfortunately
> > >  > not exactly what I meant. To be more precise:
> > >  >
> > >  > I want to point Galaxy to download (test) MS data files
> > >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> > >  >
> > >  > For that I need an ftp/http/https link to the files,
> > >  > and I was able to use
> > >  >
> > >  >
> > >
> > >
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> > >  >
> > >  > (which still works, but is probably outdated)
> > >  > So is there anything equivalent in the new git setup ?
> > >
> > > no, not from git.bioconductor.org 
> > > ;.
> > >
> > > Martin
> > >
> > >  >
> > >  > Yours,
> > >  > Steffen
> > >  >
> > >  >
> > >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> > >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> > >  >>> Hi,
> > >  >>>
> > >  >>> I would like to have a URL to individual files
> > >  >>> we have in BioC packages. This is useful
> > >   

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

this is a follow-up to a rather old thread, but with 
Mike Smith's (twitter: @grimbough) 

https://code.bioconductor.org/

We now have exactly what I had been looking for. 
Thanks Mike and BioC team !

Yours,
Steffen

On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > So, what if there was a MetaBioconductor site and repo similar to
> > the 
> > MetaCRAN project? https://www.r-pkg.org/about
> > 
> > Not sure exactly who maintains it (probably someone at RStudio),
> > but it 
> > is largely automatic I believe, and it provides a full GitHub
> > archive of 
> > *all* the packages on CRAN, which if this were done for
> > Bioconductor 
> > would satisfy what I think Steffen is looking for, as well as lots
> > of 
> > other advantages.
> > 
> > It also has the advantage that it looks like 90% of the work would
> > be 
> > done for Bioconductor with likely very little work required for
> > the 
> > Bioconductor Admins (ideally 100% of work would be done for them).
> 
> there has been some discussion of that, e.g.,
> 
>
> https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> 
> but we will not do it (maintain a github mirror), for instance
> because 
> some experiment data packages have commits that would require lfs, 
> because of issues with reliably  syncing data, and because of
> confusion 
> it introduces on the 'official' repository.
> 
> We do intend to provide a browsable interface to the official 
> git.bioconductor.org that would allow Steffen's use case during the 
> present release cycle; it is not currently available.
> 
> A different solution would be to update the relevant ExperimentData 
> package to use ExperimentHub (see, e.g., 
> https://github.com/LTLA/TENxBrainData for a relatively simple
> example, 
> though not yet in Bioconductor) and the resource would then be
> available 
> at a URL https://annotationhub.bioconductor.org/fetch/...
> 
> Martin
> 
> > Just a thought.
> > 
> > -Robert
> > 
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Puller of Rabbits from Hats
> > Research Parasite
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> > 
> > Twitter: @rmflight
> > Web: rmflight.github.io 
> > ORCID: http://orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com 
> > PH 502-509-1827 
> > 
> > To call in the statistician after the experiment is done may be no
> > more 
> > than asking him to perform a post-mortem examination: he may be
> > able to 
> > say what the experiment died of. - Ronald Fisher
> > 
> > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan 
> >  > martin.mor...@roswellpark.org>> 
> > wrote:
> > 
> > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> >  > Hi,
> >  >
> >  > thanks for the answer, unfortunately
> >  > not exactly what I meant. To be more precise:
> >  >
> >  > I want to point Galaxy to download (test) MS data files
> >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> >  >
> >  > For that I need an ftp/http/https link to the files,
> >  > and I was able to use
> >  >
> >  >
> > 
> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
> >  >
> >  > (which still works, but is probably outdated)
> >  > So is there anything equivalent in the new git setup ?
> > 
> > no, not from git.bioconductor.org 
> > ;.
> > 
> > Martin
> > 
> >  >
> >  > Yours,
> >  > Steffen
> >  >
> >  >
> >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> >  >>> Hi,
> >  >>>
> >  >>> I would like to have a URL to individual files
> >  >>> we have in BioC packages. This is useful
> >  >>> e.g. if I need test data from, say, the msdata package,
> >  >>> in another context.
> >  >>>
> >  >>> In the SVN days, I was able to point directly
> >  >>> into the SVN repo with readonly:readonly access.
> >  >>> We also had the (now deprecated) way to link to:
> >  >>> 
> > https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> >  >>> ESCRIPTION
> >  >>>
> >  >>> -> Is there anything comparable today ?
> >  >>
> >  >> I think the git archive command might do the trick, but it
> > requires
> >  >> ssh
> >  >> (i.e., write) access to the repository
> >  >>
> >  >> git archive --remote=g...@git.bioconductor.org:packages/xcms
> > \
> >  >>master DESCRIPTION | tar -xf -
> >  >>
> >  >>
> >  >>>
> >  >>> It could be as simple as a directory tree
> >  >>> of a working copies of all https://git.bioconductor.org/