[Bioc-devel] Package check errors Fwd: seqArchR problems reported in the Multiple platform build/check report for BioC 3.21
Hi,
I have installed scikit-learn at Tuesday:
biocbuild at 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 at 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 at 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 at r-project.org> on behalf of Martin Grigorov <mgrigorov at apache.org> *Sent:* Monday, December 9, 2024 3:34 AM *To:* Sarvesh Nikumbh <sarvesh.nikumbh at gmail.com> *Cc:* Bioc-devel <bioc-devel at 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 at 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 at 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 at 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:
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
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* It is possible that the problems reported in this report are false
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Thanks for contributing to the Bioconductor project! -- thanks! -Sarvesh -------------------------------------------- Q: Why is this email five sentences or less? A:
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