[Bioc-devel] Package check errors Fwd: seqArchR problems reported in the Multiple platform build/check report for BioC 3.21

Martin Grigorov mgr|gorov @end|ng |rom @p@che@org
Fri Dec 27 16:07:10 CET 2024 

Hi,

After reboot it still fails with "cannot find an open port".
I looked closer to the error logs at
https://bioconductor.org/checkResults/3.21/bioc-LATEST/seqArchR/kunpeng2-checksrc.html
and I think the error actually is:
============================================
Error in python_config_impl(python) :
  Error running '/home/biocbuild/.virtualenvs/r-reticulate/bin/python': No
such file.
The Python installation used to create the virtualenv has been moved or
removed:
============================================

biocbuild using kunpeng2 ~/git [1]> ll
/home/biocbuild/.virtualenvs/r-reticulate/bin/
total 64K
-rw-r--r-- 1 biocbuild biocbuild 1.9K Feb  5  2024 activate
-rw-r--r-- 1 biocbuild biocbuild  873 Feb  5  2024 activate.csh
-rw-r--r-- 1 biocbuild biocbuild 2.0K Feb  5  2024 activate.fish
-rw-r--r-- 1 biocbuild biocbuild 8.7K Feb  5  2024 Activate.ps1
-rwxr-xr-x 1 biocbuild biocbuild  288 Apr 27  2024 convert-caffe2-to-onnx*
-rwxr-xr-x 1 biocbuild biocbuild  288 Apr 27  2024 convert-onnx-to-caffe2*
-rwxr-xr-x 1 biocbuild biocbuild  252 Feb  5  2024 f2py*
-rwxr-xr-x 1 biocbuild biocbuild  241 Apr 27  2024 isympy*
-rwxr-xr-x 1 biocbuild biocbuild  257 Feb  5  2024 pip*
-rwxr-xr-x 1 biocbuild biocbuild  257 Feb  5  2024 pip3*
-rwxr-xr-x 1 biocbuild biocbuild  257 Feb  5  2024 pip3.10*
-rwxr-xr-x 1 biocbuild biocbuild  257 Feb  5  2024 pip3.9*
lrwxrwxrwx 1 biocbuild biocbuild    9 Feb  5  2024 python -> python3.9
lrwxrwxrwx 1 biocbuild biocbuild    9 Feb  5  2024 python3 -> python3.9
lrwxrwxrwx 1 biocbuild biocbuild   18 Feb  5  2024 python3.9 ->
/usr/bin/python3.9
-rwxr-xr-x 1 biocbuild biocbuild  256 Apr 27  2024 torchrun*
-rwxr-xr-x 1 biocbuild biocbuild  244 Feb  5  2024 wheel*

python3.9 !!

The OS provides python3.11 after the last updates. I've updated the
symlinks to use /usr/bin/python3.11 !
Let's see what the next build will show!


On Fri, Dec 27, 2024 at 11:35 AM Martin Grigorov <mgrigorov using apache.org>
wrote:

> Hi,
>
> I have installed scikit-learn at Tuesday:
>
> biocbuild using kunpeng2 ~/git [1]> python -m pip install scikit-learn
> Requirement already satisfied: scikit-learn in
> /home/biocbuild/miniconda3/lib/python3.11/site-packages (1.6.0)
> Requirement already satisfied: numpy>=1.19.5 in
> /home/biocbuild/miniconda3/lib/python3.11/site-packages (from scikit-learn)
> (2.2.1)
> Requirement already satisfied: scipy>=1.6.0 in
> /home/biocbuild/miniconda3/lib/python3.11/site-packages (from scikit-learn)
> (1.14.1)
> Requirement already satisfied: joblib>=1.2.0 in
> /home/biocbuild/miniconda3/lib/python3.11/site-packages (from scikit-learn)
> (1.4.2)
> Requirement already satisfied: threadpoolctl>=3.1.0 in
> /home/biocbuild/miniconda3/lib/python3.11/site-packages (from scikit-learn)
> (3.5.0)
>
> Since then the check fails with:
>
> biocbuild using kunpeng2 ~/git> R CMD check seqArchR_1.11.0.tar.gz
> * using log directory ‘/home/biocbuild/git/seqArchR.Rcheck’
> * using R Under development (unstable) (2024-11-24 r87369)
> * using platform: aarch64-unknown-linux-gnu
> * R was compiled by
>     aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
>     GNU Fortran (GCC) 14.2.0
> * running under: openEuler 24.03 (LTS)
> * using session charset: UTF-8
> * checking for file ‘seqArchR/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘seqArchR’ version ‘1.11.0’
> * package encoding: UTF-8
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘seqArchR’ can be installed ... OK
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking ‘build’ directory ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking for left-over files ... OK
> * checking index information ... OK
> * checking package subdirectories ...Warning: program compiled against
> libxml 212 using older 211
>  OK
> * checking code files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ...
> OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking whether the namespace can be loaded with stated dependencies
> ... OK
> * checking whether the namespace can be unloaded cleanly ... OK
> * checking loading without being on the library search path ... OK
> * checking whether startup messages can be suppressed ... OK
> * checking dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... OK
> * checking Rd metadata ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... OK
> * checking installed files from ‘inst/doc’ ... OK
> * checking files in ‘vignettes’ ... OK
> * checking examples ... OK
> * checking for unstated dependencies in ‘tests’ ... OK
> * checking tests ...
>   Running ‘testthat.R’
>  ERROR
> Running the tests in ‘tests/testthat.R’ failed.
> Last 13 lines of output:
>   ══ Failed tests
> ════════════════════════════════════════════════════════════════
>   ── Error ('test_seqArchR_main.R:149:5'): seqArchR (cv) works when
> timeFlag is FALSE ──
>   Error:   cannot find an open port. For manually specifying the port, see
>     ?SnowParam
>   Backtrace:
>       ▆
>    1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:149:5
>    2.   └─seqArchR:::perform_setup(...)
>    3.     └─BiocParallel::MulticoreParam(workers = crs, tasks = crs)
>    4.       └─BiocParallel:::.snowPort()
>    5.         └─BiocParallel:::.stop("cannot find an open port. For
> manually specifying the port, see ?SnowParam")
>
>   [ FAIL 1 | WARN 1 | SKIP 4 | PASS 104 ]
>   Error: Test failures
>   Execution halted
> * checking for unstated dependencies in vignettes ... OK
> * checking package vignettes ... OK
> * checking re-building of vignette outputs ... OK
> * checking PDF version of manual ... OK
> * DONE
>
> Status: 1 ERROR
> See
>   ‘/home/biocbuild/git/seqArchR.Rcheck/00check.log’
> for details.
>
> It is not clear to me which port it tries to use and why the official
> build run still does not see scikit-learn ...
> I will reboot the VM once the daily build finishes later today and try
> again!
>
> On Thu, Dec 26, 2024 at 9:15 PM Jennifer Wokaty <
> Jennifer.Wokaty using sph.cuny.edu> wrote:
>
>> Hi,
>>
>> All builds passing now, except for an issue with kunpeng2, which I'm
>> discussing with Martin on #arm-linux on the community Slack. I may invite
>> you to join us there if we get stuck.
>>
>>
>> Jennifer Wokaty (they/them)
>>
>> Waldron Lab at CUNY SPH
>> Bioconductor Core Team
>> ------------------------------
>> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
>> Martin Grigorov <mgrigorov using apache.org>
>> *Sent:* Monday, December 9, 2024 3:34 AM
>> *To:* Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com>
>> *Cc:* Bioc-devel <bioc-devel using r-project.org>
>> *Subject:* Re: [Bioc-devel] Package check errors Fwd: seqArchR problems
>> reported in the Multiple platform build/check report for BioC 3.21
>>
>> * This email originates from a sender outside of CUNY. Verify the sender
>> before replying or clicking on links and attachments. *
>>
>> Hi,
>>
>> This issue should be fixed on kunpeng2 in the next build run (the results
>> will be available two days from now).
>>
>> Regards,
>> Martin
>>
>> On Tue, Dec 3, 2024 at 7:58 PM Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com
>> >
>> wrote:
>>
>> > Dear Bioc team,
>> >
>> > I am seeing check errors on nebbiolo1 and palomino7 and build and
>> install
>> > error on kunpeng2 for my package "seqArchR". The check errors are due to
>> > the missing Python module scikit-learn, and others are due to
>> dependencies
>> > not being available. I believe this is being looked into by the team.
>> > Please let me know if you need anything from my side to get this
>> resolved.
>> >
>> > Thanks and best wishes,
>> >   Sarvesh
>> >
>> >
>> > ---------- Forwarded message ---------
>> > From: <BBS-noreply using bioconductor.org>
>> > Date: Tue, 3 Dec 2024 at 22:30
>> > Subject: seqArchR problems reported in the Multiple platform build/check
>> > report for BioC 3.21
>> > To: <sarvesh.nikumbh using gmail.com>
>> >
>> >
>> > [This is an automatically generated email. Please don't reply.]
>> >
>> > Hi seqArchR maintainer,
>> >
>> > According to the Multiple platform build/check report for BioC 3.21,
>> > the seqArchR package has the following problem(s):
>> >
>> >   o ERROR for 'R CMD check' on nebbiolo1. See the details here:
>> >
>> >
>> >
>> https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/seqArchR/nebbiolo1-checksrc.html__;!!LRXxDv2l!SAm81ssftyYCFtEnWDLRGhmNLFYQviFOkWffrugLy_nNcfjwOCASVtR1LMdj9ZYFn9I03NRsIbuvToqCRon2i_GuHmcXzA$
>> >
>> > Please take the time to address this by committing and pushing
>> > changes to your package at git.bioconductor.org
>> >
>> > Notes:
>> >
>> >   * This was the status of your package at the time this email was sent
>> to
>> > you.
>> >     Given that the online report is updated daily (in normal conditions)
>> > you
>> >     could see something different when you visit the URL(s) above,
>> > especially if
>> >     you do so several days after you received this email.
>> >
>> >   * It is possible that the problems reported in this report are false
>> > positives,
>> >     either because another package (from CRAN or Bioconductor) breaks
>> your
>> >     package (if yours depends on it) or because of a Build System
>> problem.
>> >     If this is the case, then you can ignore this email.
>> >
>> >   * Please check the report again 24h after you've committed your
>> changes
>> > to the
>> >     package and make sure that all the problems have gone.
>> >
>> >   * If you have questions about this report or need help with the
>> >     maintenance of your package, please use the Bioc-devel mailing list:
>> >
>> >
>> https://urldefense.com/v3/__https://bioconductor.org/help/mailing-list/__;!!LRXxDv2l!SAm81ssftyYCFtEnWDLRGhmNLFYQviFOkWffrugLy_nNcfjwOCASVtR1LMdj9ZYFn9I03NRsIbuvToqCRon2i_GWDRO4ew$
>> >
>> >     (all package maintainers are requested to subscribe to this list)
>> >
>> > For immediate notification of package build status, please
>> > subscribe to your package's RSS feed. Information is at:
>> >
>> >
>> https://urldefense.com/v3/__https://bioconductor.org/developers/rss-feeds/__;!!LRXxDv2l!SAm81ssftyYCFtEnWDLRGhmNLFYQviFOkWffrugLy_nNcfjwOCASVtR1LMdj9ZYFn9I03NRsIbuvToqCRon2i_HCYkxsMQ$
>> >
>> > Thanks for contributing to the Bioconductor project!
>> >
>> >
>> >
>> > --
>> >
>> > thanks!
>> > -Sarvesh
>> >
>> > --------------------------------------------
>> > Q: Why is this email five sentences or less?
>> > A:
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