Hi,
I have installed scikit-learn at Tuesday:
biocbuild@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@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.wok...@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-boun...@r-project.org> on behalf of Martin
> Grigorov <mgrigo...@apache.org>
> *Sent:* Monday, December 9, 2024 3:34 AM
> *To:* Sarvesh Nikumbh <sarvesh.niku...@gmail.com>
> *Cc:* Bioc-devel <bioc-devel@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.niku...@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-nore...@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.niku...@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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