Re: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2
Hi Stijn, Note that today the error is gone. This is a race condition in 'R CMD check' that affects some packages on Windows. What 'R CMD check' is trying to do here is open the msqrob2-Ex.Rout file but that file is still being written to by another process. Windows (unlike Linux or macOS) doesn't like that: it won't let a process open a file if the file is being hold by another process. More precisely here is what is happening here: - One of the checks that 'R CMD check' performs is to run all the examples in a package, and to capture the output produced by the examples in a file (the msqrob2-Ex.Rout in your case). - Once it's done running the examples, 'R CMD check' wants to know if the examples produced errors. It does this by parsing the msqrob2-Ex.Rout file. That's when it tries to open the file in read-only mode. - But sometimes, when 'R CMD check' tries to open msqrob2-Ex.Rout in read-only mode, other processes are still holding on the msqrob2-Ex.Rout file. This typically happens when the examples in the package spawn subprocesses. For example these spawned processes can be the workers spawned by BiocParallel or by other parallel evaluation mechanism (e.g. doParallel/foreach). Note that there can be a very small lag between the moment the main worker and the spawned workers are done. If one of the spawned workers takes a fraction of an extra second to finish writing some output to msqrob2-Ex.Rout, then 'R CMD check' won't be able to open the file. One could argue that this is an issue with 'R CMD check'. Maybe on Windows it should wait a couple of seconds before trying to open msqrob2-Ex.Rout, I don't know. Maybe there's something that could be done in BiocParallel too. I don't know how hard that would be, or if that's even feasible, but maybe there's a way that the main worker could wait and make sure that all the spawn processes are dead before returning. I guess that kind of feature would only make sense for some parallel back-ends. Does some of the examples in msqrob2 use parallelization? If so maybe you can try to add a call to Sys.sleep(2) at the end of those examples and see if that helps. In any case there's nothing that can really be done on our Windows builders to prevent this, sorry. Hope this helps, H. On 28/10/2022 06:29, vandenbulcke stijn wrote: Dear All, On the palomino4 host the check for msqrob2 returns the following error ( http://bioconductor.org/checkResults/devel/bioc-LATEST/msqrob2/palomino4-checksrc.html ) * checking examples ...Warning in file(con, "r") : cannot open file 'msqrob2-Ex.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted I am however not able to reproduce this, and it works on the other hosts. Would anyone know the cause of this issue? Thanks in advance Stijn [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Check error after deadline
Yes the package will stay in the release. We say today to fix ERROR's because it will guarantee a run on the daily builder and build report. After this time changes pushed may not be reflected before we branch and then any remaining ERRORs may need to be applied to the RELEASE_3_16 branch (created next Tuesday for all package by the core team) and the master (devel) branch. In general, if we know that maintainers are actively trying to fix a package we will not deprecate and it will remain in the release. Lori Shepherd - Kern 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 Burak Ogan Mancarci Sent: Friday, October 28, 2022 12:08 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Check error after deadline Hi, On the release schedule ( https://secure-web.cisco.com/1MuZMLBOSidorwdc-i0rEc71hYGPikoZNFOaC8Xa_Yfu2lP_t_nkZdWS_vT998Mp1jj2uGofsq8sUTfY2kH02JI-wl7g4OgeWMtmMhY6nWdhHNSI2MApMe8sViNxX0-za6cif2jmY-vBz7_w8E46mLEruDDheaka14Vza5QHO6QwBtHacdACSe-95ZfSywisr_xkNbuL13lYXtFgZmNYXs9zkbYzVXnOoKK6pCiV7MKQI4kBk7u9XtuvaQ5XbwtPmGBOiJDG1b_6akKWEH6cpRzgTuBihtIDquyCF4-m5r9Xm8noOr2qayDBNTSndnMAL/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Frelease-schedule%2F) it was stated that the last day to pass without errors was 28th. In the latest build of gemma.R triggered by changes to documentation, we got a connection timeout error when communicating with the API that the package wraps in the MacOS test. I was wondering if it was possible to make it to the release regardless. A re-try will fix the issue. Problematic build: http://secure-web.cisco.com/1oK3fXzrxW6IQeORpAiyB5xx6uYVjF-tMGr-DGa6D_2TFrT9fRNNf_SbDGRh_NnC8N0f-zm_OFl02Y5PQh9aI2bYy4tNyKwvTAbIT6lTrO4tWUaP5vskXC1yIHHKkj_oioRuW12Pzk8P5CsDK_BSaShZ91RZ5gyn2P-ousCYFu3oy8zrOvfNPYQKBx46XfVLKOfkC9z4GShmZXLj0oKot9o2mi9bfWGa64QLbBzzQznwSAYL9jfnW60kqe69l5VK2RSRkR3-YbtBuFsRo2z7FgXXGO0KjOpnXwG679c4XS6-2IZhF3NDUKlWBVeoMb79E/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fgemma.R%2Flconway-checksrc.html Cheers, Ogan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1sMV82EBxgm8c5TBT8CEMuqmHdMI0HEgFXTb2GTGMsTOwhySdgXGqWWkiSSf9265yYVFJ4WYRmzW5AGgBxvmwnhECKwawz2T-C6iTnGYSSG1y6hWaoiZ3kV9bBfD_HKgiMjMnTKf6u9327iao3ybpfXSR3H2aZq_uznY0UZUEZ8r8BPqKnx9Li7fpHdrF07jd2e34GjHOskphW7mFH9QyMb64d-GX9kCSNJc1uIU10AYSGWaIDPjLb-v9jOsA0AWIPybAKiVMEx1HeFQxOAy0mirV-WBfzURcL4AwBK2nggqnoSxkPktRPV377l8_XJSa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Check error after deadline
Hi, On the release schedule ( https://bioconductor.org/developers/release-schedule/) it was stated that the last day to pass without errors was 28th. In the latest build of gemma.R triggered by changes to documentation, we got a connection timeout error when communicating with the API that the package wraps in the MacOS test. I was wondering if it was possible to make it to the release regardless. A re-try will fix the issue. Problematic build: http://bioconductor.org/checkResults/devel/bioc-LATEST/gemma.R/lconway-checksrc.html Cheers, Ogan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] seqArchR error on build systems
Ubuntu and macOS errors are now fixed, but the palomino4/Windows error
is still there (this error is different), says, it needs OpenSSL.
Thanks in advance.
===
Collecting package metadata (current_repodata.json): ...working...
Collecting package metadata (current_repodata.json): ...working...
failed
CondaSSLError: OpenSSL appears to be unavailable on this machine.
OpenSSL is required to
download and install packages.
Exception: HTTPSConnectionPool(host='conda.anaconda.org', port=443):
Max retries exceeded with url:
/conda-forge/win-64/current_repodata.json (Caused by SSLError("Can't
connect to HTTPS URL because the SSL module is not available."))
+ "C:/Users/biocbuild/AppData/Local/r-miniconda/condabin/conda.bat"
"create" "--yes" "--prefix"
"C:/Users/biocbuild/AppData/Local/r-miniconda/envs/r-reticulate"
"python=3.8" "numpy" "--quiet" "-c" "conda-forge"
failed
CondaSSLError: OpenSSL appears to be unavailable on this machine.
OpenSSL is required to
download and install packages.
Exception: HTTPSConnectionPool(host='conda.anaconda.org', port=443):
Max retries exceeded with url:
/conda-forge/win-64/current_repodata.json (Caused by SSLError("Can't
connect to HTTPS URL because the SSL module is not available."))
===
Thanks and best,
Sarvesh
On Tue, 25 Oct 2022 at 22:05, Hervé Pagès wrote:
>
> Hi Sarvesh,
>
> It looks like reticulate somehow was using the wrong Python instance on
> nebbiolo2 and lconway, as reported by py_config().
>
> We're now setting RETICULATE_PYTHON on those machines to make sure that
> reticulate will use the correct Python. This change was made after the
> builds started today so it won't be reflected on tomorrow's report. But
> it should be reflected on Thursday's report.
>
> We'll do the same on the other build machines soon.
>
> Best,
>
> H.
>
> On 25/10/2022 08:53, Sarvesh Nikumbh wrote:
> > Hi Bioc-team,
> >
> > seqArchR was building fine, without any errors last week, but I am seeing
> > an error again. This time it is due to the Python module 'sklearn' not
> > available and one another error. The sklearn-related error occurs on
> > nebbiolo2 and Iconway, while palomino4 shows a different error.
> >
> > Maybe something changed on the build systems? Because these system
> > requirements were available before*.*
> >
> > Thanks and best,
> >Sarvesh
> >
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
--
thanks!
-Sarvesh
Q: Why is this email five sentences or less?
A: http://five.sentenc.es
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Re: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2
Thanks for your email. I'll look into this. From: Bioc-devel on behalf of vandenbulcke stijn Sent: Friday, October 28, 2022 9:29 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear All, On the palomino4 host the check for msqrob2 returns the following error ( https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_msqrob2_palomino4-2Dchecksrc.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HNeyisXM7SP-moqvWWnaXru04ziiE1kXfXFE43gC6oe4eq79u7VxKHBWxpknrTwU=F79QOTCx_p3FTiKuMas7dkAWWqpkE84sGvg3QWSDqZY= ) * checking examples ...Warning in file(con, "r") : cannot open file 'msqrob2-Ex.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted I am however not able to reproduce this, and it works on the other hosts. Would anyone know the cause of this issue? Thanks in advance Stijn [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HNeyisXM7SP-moqvWWnaXru04ziiE1kXfXFE43gC6oe4eq79u7VxKHBWxpknrTwU=Zu4D5KpYLpfevsh0dKoPEj2D7gj0t842cfe8ODlO_9k= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] palomino4 CHECK error "permission denied" msqrob2
Dear All, On the palomino4 host the check for msqrob2 returns the following error ( http://bioconductor.org/checkResults/devel/bioc-LATEST/msqrob2/palomino4-checksrc.html ) * checking examples ...Warning in file(con, "r") : cannot open file 'msqrob2-Ex.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted I am however not able to reproduce this, and it works on the other hosts. Would anyone know the cause of this issue? Thanks in advance Stijn [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
