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
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Error: Bioconductor Git Credentials

[Turaga, Nitesh]

The email registered is rvs.bioto...@gmail.com.

You have to first activate it before you can access it, as you have never 
signed in before. 
https://git.bioconductor.org/BiocCredentials/account_activation/

Please check your spam email as well. 

> On Jan 21, 2020, at 2:41 PM, Richard Virgen-Slane  
> wrote:
> 
> Hi,
> 
> I'm the maintainer of GmicR.  I'm unable to access/activate my Bioconductor
> Git Credentials.
> 
> Whenever I try to log on, it says that my email address is not associated
> as a package maintainer.  I'm using the same email address that is
> receiving the build reports.
> 
> Any suggestions?
> 
> Richard
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Error: Bioconductor Git Credentials

[Richard Virgen-Slane]

Hi,

I'm the maintainer of GmicR.  I'm unable to access/activate my Bioconductor
Git Credentials.

Whenever I try to log on, it says that my email address is not associated
as a package maintainer.  I'm using the same email address that is
receiving the build reports.

Any suggestions?

Richard

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

[Shepherd, Lori]

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 

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]]
>
> ___
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>
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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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>
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Re: [Bioc-devel] Rhtslib-linked package not compiling on Windows

[Pages, Herve]

Hi Lucas,

In order to compile an Rhtslib client package on Windows you need a 
setup that mimics closely what we have on our Windows builders. In 
particular you need to install a bunch of external libraries in 
C:\extsoft and edit R\etc\i386\Makeconf and R\etc\x64\Makeconf to let R 
know about these external libraries. The exact setup is documented here:

 
https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-Windows-Server-2012-HOWTO.md

End users don't need any of this because they typically install the 
Windows package binaries which are statically linked.

Unfortunately, if Windows is the platform where you intend to develop 
your package, you'll have to go thru the complicated setup described 
above. Alternatively, if that's an option for you, you could develop 
your package on Linux. Installing the external libraries there is very 
easy so the development process will be a lot easier. Then, when you 
summit your package to Bioconductor, we'll start building the Windows 
and Mac binaries for you so you'll get build reports for these 
platforms. Also, once the package is accepted, we'll distribute the 
Windows and Mac binaries so on these platforms your users won't need any 
of the external dependencies.

Hope this helps,

H.

On 1/20/20 14:09, Lucas Nell wrote:
> Hello,
> 
> I'm having trouble linking to Rhtslib on Windows, specifically with finding
> some of the required linked libraries (libcurl, among others). I made a
> simple R package with only one function that compresses a file using BGZF
> (link here 
>   >). After reading
> through the Rhtslib instructions again, I tried building the package on
> Windows 10 and got the output below. The directory C:/extsoft does not
> exist, so I feel like there's something else I need to install.
> 
> Thanks for your help! (And thank you to the Rhtslib creators for a super
> useful package!)
> 
> Cheers,
> Lucas
> 
> 
> ==> Rcpp::compileAttributes()
> 
> * Updated R/RcppExports.R
> 
> ==> Rcmd.exe INSTALL --preclean --no-multiarch --with-keep.source
> RhtslibTest
> 
> * installing to library 'C:/Users/acuit/Documents/R/win-library/3.6'
> * installing *source* package 'RhtslibTest' ...
> ** using staged installation
> ** libs
> C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-36~1.2/include"
> -DNDEBUG -D_FILE_OFFSET_BITS=64
> -I"C:/Users/acuit/Documents/R/win-library/3.6/Rcpp/include"
> -I"C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/include"
> -I"C:/Users/acuit/Documents/R/win-library/3.6/zlibbioc/include"-O2
> -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
> C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-36~1.2/include"
> -DNDEBUG -D_FILE_OFFSET_BITS=64
> -I"C:/Users/acuit/Documents/R/win-library/3.6/Rcpp/include"
> -I"C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/include"
> -I"C:/Users/acuit/Documents/R/win-library/3.6/zlibbioc/include"-O2
> -Wall  -mtune=generic -c write_bgzf.cpp -o write_bgzf.o
> write_bgzf.cpp: In function 'int compress_file(const string&, const int&)':
> write_bgzf.cpp:54:9: warning: variable 'in_code' set but not used
> [-Wunused-but-set-variable]
>   int in_code;
>   ^
> C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
> RhtslibTest.dll tmp.def RcppExports.o write_bgzf.o
> C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/usrlib/x64/libhts.a
> -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz
> -lws2_32 -lwldap32 -lwinmm -LC:/PROGRA~1/R/R-36~1.2/bin/x64 -lR
> C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lcurl
> C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lrtmp
> C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lssl
> C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lssh2
> C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lcrypto
> collect2.exe: error: ld returned 1 exit status
> no DLL was created
> ERROR: compilation failed for package 'RhtslibTest'
> * removing 'C:/Users/acuit/Documents/R/win-library/3.6/RhtslibTest'
> 
> Exited with status 1.
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] New bioconductor_docker image officially released

[Turaga, Nitesh]

Hello developers,

The new "bioconductor/bioconductor_docker" image is officially released.

The link to access it on Dockerhub is:  
https://hub.docker.com/repository/docker/bioconductor/bioconductor_docker.

The source code in on GitHub at: 
https://github.com/bioconductor/bioconductor_docker.

Please note there are currently two versions,

1. bioconductor/bioconductor_docker:devel

2. bioconductor/bioconductor_docker:RELEASE_3_10 or 
bioconductor/bioconductor_docker:latest

The previous set of images have been deprecated. The previous images have also 
been updated with a `LABEL` in the Dockerfile which refers to them as 
"Deprecated". You can see this information on your image if you do a  `docker 
pull ; docker inspect `. Please note, we will support 
these images through this release cycle.

We highly recommend that you shift to the new images, and use those containers. 
They come with all the system dependencies to install almost all of the 
Bioconductor packages, an RStudio interface, and with customizations which are 
specific to Bioconductor.

Docker images are now considered similar to Bioconductor packages. There will 
be official contributions from the community following our list of best 
practices.
 If you need more information on the docker images please refer to 
http://bioconductor.org/help/docker/.

As always, if you have any questions, please feel free to reply to this email.

Best regards,

Nitesh





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[Bioc-devel] Devel Build Report

[Shepherd, Lori]

Hello all,

We are experiencing some issues with our mac builder that has caused the build 
report not to be generated over the weekend.
We will temporarily be excluding the mac builder (celaya2)  in the devel build 
report until the issue is resolved.  This should also allow a build report to 
be generated daily for the linux (malbec2) and tokay2 (windows) builders.  
Daily build reports should resume for the devel builder today or tomorrow.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] DeMixT issue

[Shepherd, Lori]

We noticed the build report has not been updated since Fri Jan 17th.   We have 
corrected the issue and there should be a new report today or tomorrow.

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 Shepherd, Lori 

Sent: Tuesday, January 21, 2020 9:06 AM
To: py11 ; Martin Morgan 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] DeMixT issue

The current version on devel is 1.3.2 which is what is consistent with what is 
in
g...@git.bioconductor.org:packages/DeMixT.git

If you would like updates you need to update your version to 1.3.3  in the next 
round of changes.


As Martin said previously,  the landing page will not update until you have a 
successful build.  You can see from the build report,  the package is still 
timing out using version 1.3.2
http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
Therefore the landing page remains at 1.3.1

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 py11 

Sent: Monday, January 20, 2020 3:11 PM
To: Martin Morgan 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] DeMixT issue

Hello,

I pushed my updated package into biconductor master branch on Jan
18th; however, I still didn't see the version change in devel branch
as follow:

https://bioconductor.org/packages/devel/bioc/html/DeMixT.html

May I ask where can I find the build report for the latest update?

Thanks,
Peng

Quoting Martin Morgan :

> The package is always built from the current git repository,
> regardless of version. So your package will build.
>
> A successfully built package (passing install / build / check) is
> only 'pushed' to the public repository if the version is different
> (higher) than the current published repository. Your original 1.3.2
> version has not built successfully, it has not been pushed. If your
> new 1.3.2 version builds successfully, it will be pushed.
>
> BUT the best practice is simply to increment the version, so that
> there is no confusion -- in the previous paragraph I had to say
> 'your original 1.3.2 version' and 'your new 1.3.2 version', but it
> would have been much clearer to say version 1.3.2 and 1.3.3.
>
> Martin
>
> On 1/18/20, 5:39 PM, "py11"  wrote:
>
> Hi Martin,
>
> Thank you very much for the detailed report. I have noticed in the report
>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
>
> the build failed due to check out of time. I re-arrange the examples
> in my Rd file, which guarantee the run time of R CMD check lower than
> 10 mins. So I pushed the package again into bioconductor with version
> 1.3.2 again. And my question is, is 1.3.2 the right version that I am
> using for and will it be built in the following night?
>
> Note the current devel version in our package page is 1.3.1 as shown
> in link below:
>
> https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>
> Thanks,
> Peng
>
>
>
> Quoting Martin Morgan :
>
> > I see
> >
> > DeMixT master$ grep Version DESCRIPTION
> > Version: 1.3.2
> >
> > Which is fine.
> >
> > Remember that accepted Bioconductor packages are *built nightly*
> > rather than on commit. This ensures that the current version of your
> > package is working with the current version of all other packages in
> > the Bioconductor ecosystem, and that that other Bioconductor
> > packages that may depend on your package are working with it.
> >
> > Look at the build report for your package
> >
> >   https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
> >
> > Note the publication date, which is when the last nightly build
> > completed and the build report created
> >
> >   This page was generated on 2020-01-15 11:54:40 -0500 (Wed,
> 15 Jan 2020).
> >
> > Note the Snapshot date, the date and time when a clone of your
> > repository was made to start the nightly build
> >
> >   Snapshot Date: 2020-01-14 16:46:51 -0500 (Tue, 14 Jan 2020)
> >
> > Finally, note from your repository the date of your last commit
> >
> >   DeMixT master$ git log -n 1
> >   commit e86bea0d14ac39f3d019f8aed3612747acabb55f
> >   Author: pengyang0411 <57335942+pengyang0...@users.noreply.github.com>
> >   Date:   Wed Jan 15 14:27:55 2020 -0600
> >
> > Your commit was after the most recent nightly build started, so the
> > changes have not yet been incorporated into the build. Wait for the
> > next nightly build (starting at about 5pm Eastern time, ending
> > Tomorrow at about noon US eastern time) 

Re: [Bioc-devel] DEWSeq: Multiple platform build failures

[Biohentze]

Hi Lori,
Didn't realize that it was reported before.
Many thanks for your response
Sudeep.
On Tue, 2020-01-21 at 14:12 +, Shepherd, Lori wrote:
> Please see Martin's response 
> 
> 
> 
> 
> 
> https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016049.html
> 
> 
> 
> 
> 
> 
> 
> It looks like there is progress on the open issue on knitr so hopefully this 
> should clear up soon.  
> 
> https://github.com/yihui/knitr/issues/1797
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> I don't believe you have to do anything on your end at this time and it is 
> indeed an issue with a dependency. 
> 
> 
> 
> 
> 
> 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 Biohentze 
> 
> 
> Sent: Tuesday, January 21, 2020 2:10 AM
> 
> To: bioc-devel@r-project.org 
> 
> Subject: [Bioc-devel] DEWSeq: Multiple platform build failures
>  
> 
> 
> Hi all,
> 
> 
> 
> We received a build report that our package failed to build on all the 
> platforms (
> 
> https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/DEWSeq/malbec1-buildsrc.html).
>  There has been a similar mail last Friday, but that wasthe
>  first time we received such a build report. 
> 
> But as you can see from the build report, the last change to the package was 
> on October 29th and we only started receiving build failure reports last
> 
> Friday. So most likely this is a build system issue. Could you please take a 
> look at this issue ?
> 
> 
> 
> Thank you.
> 
> 
> 
> Sudeep.
> 
> 
> 
> [[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.  
> 

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Re: [Bioc-devel] DEWSeq: Multiple platform build failures

[Shepherd, Lori]

Please see Martin's response

https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016049.html

It looks like there is progress on the open issue on knitr so hopefully this 
should clear up soon.
https://github.com/yihui/knitr/issues/1797


I don't believe you have to do anything on your end at this time and it is 
indeed an issue with a dependency.

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 Biohentze 

Sent: Tuesday, January 21, 2020 2:10 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] DEWSeq: Multiple platform build failures

Hi all,

We received a build report that our package failed to build on all the 
platforms (
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/DEWSeq/malbec1-buildsrc.html).
 There has been a similar mail last Friday, but that wasthe first time we 
received such a build report.
But as you can see from the build report, the last change to the package was on 
October 29th and we only started receiving build failure reports last
Friday. So most likely this is a build system issue. Could you please take a 
look at this issue ?

Thank you.

Sudeep.

[[alternative HTML version deleted]]

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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] DeMixT issue

[Shepherd, Lori]

The current version on devel is 1.3.2 which is what is consistent with what is 
in
g...@git.bioconductor.org:packages/DeMixT.git

If you would like updates you need to update your version to 1.3.3  in the next 
round of changes.


As Martin said previously,  the landing page will not update until you have a 
successful build.  You can see from the build report,  the package is still 
timing out using version 1.3.2
http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
Therefore the landing page remains at 1.3.1

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 py11 

Sent: Monday, January 20, 2020 3:11 PM
To: Martin Morgan 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] DeMixT issue

Hello,

I pushed my updated package into biconductor master branch on Jan
18th; however, I still didn't see the version change in devel branch
as follow:

https://bioconductor.org/packages/devel/bioc/html/DeMixT.html

May I ask where can I find the build report for the latest update?

Thanks,
Peng

Quoting Martin Morgan :

> The package is always built from the current git repository,
> regardless of version. So your package will build.
>
> A successfully built package (passing install / build / check) is
> only 'pushed' to the public repository if the version is different
> (higher) than the current published repository. Your original 1.3.2
> version has not built successfully, it has not been pushed. If your
> new 1.3.2 version builds successfully, it will be pushed.
>
> BUT the best practice is simply to increment the version, so that
> there is no confusion -- in the previous paragraph I had to say
> 'your original 1.3.2 version' and 'your new 1.3.2 version', but it
> would have been much clearer to say version 1.3.2 and 1.3.3.
>
> Martin
>
> On 1/18/20, 5:39 PM, "py11"  wrote:
>
> Hi Martin,
>
> Thank you very much for the detailed report. I have noticed in the report
>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
>
> the build failed due to check out of time. I re-arrange the examples
> in my Rd file, which guarantee the run time of R CMD check lower than
> 10 mins. So I pushed the package again into bioconductor with version
> 1.3.2 again. And my question is, is 1.3.2 the right version that I am
> using for and will it be built in the following night?
>
> Note the current devel version in our package page is 1.3.1 as shown
> in link below:
>
> https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>
> Thanks,
> Peng
>
>
>
> Quoting Martin Morgan :
>
> > I see
> >
> > DeMixT master$ grep Version DESCRIPTION
> > Version: 1.3.2
> >
> > Which is fine.
> >
> > Remember that accepted Bioconductor packages are *built nightly*
> > rather than on commit. This ensures that the current version of your
> > package is working with the current version of all other packages in
> > the Bioconductor ecosystem, and that that other Bioconductor
> > packages that may depend on your package are working with it.
> >
> > Look at the build report for your package
> >
> >   https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
> >
> > Note the publication date, which is when the last nightly build
> > completed and the build report created
> >
> >   This page was generated on 2020-01-15 11:54:40 -0500 (Wed,
> 15 Jan 2020).
> >
> > Note the Snapshot date, the date and time when a clone of your
> > repository was made to start the nightly build
> >
> >   Snapshot Date: 2020-01-14 16:46:51 -0500 (Tue, 14 Jan 2020)
> >
> > Finally, note from your repository the date of your last commit
> >
> >   DeMixT master$ git log -n 1
> >   commit e86bea0d14ac39f3d019f8aed3612747acabb55f
> >   Author: pengyang0411 <57335942+pengyang0...@users.noreply.github.com>
> >   Date:   Wed Jan 15 14:27:55 2020 -0600
> >
> > Your commit was after the most recent nightly build started, so the
> > changes have not yet been incorporated into the build. Wait for the
> > next nightly build (starting at about 5pm Eastern time, ending
> > Tomorrow at about noon US eastern time) to see your changes
> > incorporated into the build system.
> >
> > If the build is successful, then the blue 'light' at the extreme
> > right of the report will change to 'green', indicating that a new
> > version has been built. This will then trigger an update of your
> > package landing page
> >
> >   https://bioconductor.org/packages/devel/DeMixT
> >
> > A similar process occurs for the release branch, with the report and
> > landing page at
> >
> >