[Bioc-devel] Question about cstack usage error
Hi, We've been encountering a cstack related error on the build systems on random occasions (https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/ReactomeGSA/nebbiolo2-checksrc.html): Error: C stack usage 7970308 is too close to the limit I know, that the limit can be adapted using the "ulimit -s 16384" command before starting the R session. Unfortunately, in our case it seems to be caused by a call to the gplots::heatmap.2 function. Thanks a lot! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Incorrect warning about failing package built
nes
Am 2024-02-02 01:37, schrieb Hervé Pagès:
Just to clarify: we build the vignettes on all
platforms, via 'R CMD build'. However when a package
contains more than one vignette like here, keep in
mind that 'R CMD build' evaluates them all in the same
R session. This "feature" can help a vignette succeed
even if it's broken. For example if ReactomeGSA got
loaded by a previous vignette then evaluation of
reanalysing-public-data.Rmd would still succeed even
though it doesn't do 'library(ReactomeGSA)'.
To complicate things even more, it could be that the
order in which vignettes are evaluated is
platform-dependent. This could explain why a vignette
succeeds on one platform and not the other.
Best,
H.
On 2/1/24 13:30, Johannes Griss wrote:
Hi,
Thanks a lot for the quick reply!
Vignette is already fixed and committed.
Kind regards,
Johannes
On 01.02.24 22:24, Martin Grigorov wrote:
Hi,
On Thu, 1 Feb 2024 at 23:05, Jennifer Wokaty
mailto:jennifer.wok...@sph.cuny.edu>
<mailto:jennifer.wok...@sph.cuny.edu>
<mailto:jennifer.wok...@sph.cuny.edu>> wrote:
Hi Johannes,
Looking at R CMD Check on devel, it looks like
you're missing a
`library(ReactomeGSA)` in
reanalysing-public-data.Rmd, which is why
it doesn't find the function
`get_public_species()`. We only build
the vignettes on the Linux builders, which this
error is only caught
there.
Regarding the error kunpeng2, we could ask its
maintainer to install
ReactomeGSA.data, which appears to be missing.
If this happens
again, you can reach out to Martin on the Bioc
Community Slack
channel #arm-linux. He's very active and
responsive.
I will take a look early next week!
Martin
Lastly, regarding the notification that happened
on the 2024/01/08,
it's possible that it failed due to an issue
with another package at
that time which has since been resolved.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel
mailto:bioc-devel-boun...@r-project.org>
<mailto:bioc-devel-boun...@r-project.org>
<mailto:bioc-devel-boun...@r-project.org>> on behalf
of Johannes
Griss mailto:johannes.gr...@meduniwien.ac.at>
<mailto:johannes.gr...@meduniwien.ac.at>
<mailto:johannes.gr...@meduniwien.ac.at>>
Sent: Thursday, February 1, 2024 3:18 PM
To: bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Incorrect warning about
failing package built
* This email originates from a sender outside of
CUNY. Verify the
sender before replying or clicking on links and
attachments. *
Hello,
I just received a second warning the our package
ReactomeGSA is failing
in both release and devel on all platforms.
Quickly checking the respective reports shows
that this is not the case:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJB
Re: [Bioc-devel] Incorrect warning about failing package built
Hi, Thanks a lot for the quick reply! Vignette is already fixed and committed. Kind regards, Johannes On 01.02.24 22:24, Martin Grigorov wrote: Hi, On Thu, 1 Feb 2024 at 23:05, Jennifer Wokaty mailto:jennifer.wok...@sph.cuny.edu>> wrote: Hi Johannes, Looking at R CMD Check on devel, it looks like you're missing a `library(ReactomeGSA)` in reanalysing-public-data.Rmd, which is why it doesn't find the function `get_public_species()`. We only build the vignettes on the Linux builders, which this error is only caught there. Regarding the error kunpeng2, we could ask its maintainer to install ReactomeGSA.data, which appears to be missing. If this happens again, you can reach out to Martin on the Bioc Community Slack channel #arm-linux. He's very active and responsive. I will take a look early next week! Martin Lastly, regarding the notification that happened on the 2024/01/08, it's possible that it failed due to an issue with another package at that time which has since been resolved. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Johannes Griss mailto:johannes.gr...@meduniwien.ac.at>> Sent: Thursday, February 1, 2024 3:18 PM To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> mailto:bioc-devel@r-project.org>> Subject: [Bioc-devel] Incorrect warning about failing package built * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hello, I just received a second warning the our package ReactomeGSA is failing in both release and devel on all platforms. Quickly checking the respective reports shows that this is not the case: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D=0 <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D=0><https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$ <https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D=0 <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D=0><https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4n
[Bioc-devel] Incorrect warning about failing package built
Hello, I just received a second warning the our package ReactomeGSA is failing in both release and devel on all platforms. Quickly checking the respective reports shows that this is not the case: https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/ https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/ On release we have no errors or warnings at all, on devel, everything is fine in two instances while the others seem to have issues that we will look into. Is there anything I can do to fix that? Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
Hi Jennifer, Thanks a lot for the quick response! Our build server was still on an older version of Seurat. Data package is updated. Kind regards, Johannes On 06.11.23 20:30, Jennifer Wokaty wrote: Hi Johannes, I installed R 4.3.2 on the release builders on Thursday after the last Experiment package report. ReactomeGSA.data will be reinstalled tomorrow so this error will resolve soon; however, it's masking another error: ## ## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA ### ## ## * checking for file 'ReactomeGSA/DESCRIPTION' ... OK * preparing 'ReactomeGSA': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'analysing-scRNAseq.Rmd' using rmarkdown Quitting from lines 58-62 [unnamed-chunk-2] (analysing-scRNAseq.Rmd) Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: Please run UpdateSeuratObject on your object --- failed re-building 'analysing-scRNAseq.Rmd' --- re-building 'using-reactomegsa.Rmd' using rmarkdown --- finished re-building 'using-reactomegsa.Rmd' SUMMARY: processing the following file failed: 'analysing-scRNAseq.Rmd' Error: Vignette re-building failed. Execution halted Lori was able to reproduce this on her local machine and suggested that you might need to update your data object in ReactomeGSA.data. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team *From:* Bioc-devel on behalf of Johannes Griss *Sent:* Friday, November 3, 2023 4:52 PM *To:* bioc-devel@r-project.org *Subject:* [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18? * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi everyone, For a while the build system reported an error that our ReactomeGSA package cannot be build due to the missing dependency of the "ReactomeGSA.data" package which is required to build the vignettes and is listed in the "Suggests" section. ReactomeGSA.data seems to building fine though but depends on ReactomeGSA. Unfortunately, I cannot figure out how I could solve this issue. Thanks for your help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cd0b8a0d7666d4bbfc4b808dbdcaecbe7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638346415598213348%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=v2kHQF1w6Ks5q0vmoZAnNo3ZKXjLeqLnMn5Ou7NKF64%3D=0 <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4$> ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
Hi everyone, For a while the build system reported an error that our ReactomeGSA package cannot be build due to the missing dependency of the "ReactomeGSA.data" package which is required to build the vignettes and is listed in the "Suggests" section. ReactomeGSA.data seems to building fine though but depends on ReactomeGSA. Unfortunately, I cannot figure out how I could solve this issue. Thanks for your help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Deprecation of scClassifR
Hi everyone, Since scAnnotatR (the renamed version of scClassifR) is now available, we'd like to deprecate scClassifR. We'd be grateful if you could point us in the right direction. Thanks a lot! Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ReactomeGSA - SSL Certificate Error on MacOS build
Hi Jennifer, Thanks a lot for the quick response! Kind regards, Johannes On 14.10.21 15:11, Jennifer Wokaty wrote: Hi Johannes, We've updated the certificates on the release Mac builder yesterday, so we should see these issues clear up on the next release build report Friday. Jennifer Wokaty Bioconductor Core Team From: Bioc-devel on behalf of Johannes Griss Sent: Thursday, October 14, 2021 4:48 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] ReactomeGSA - SSL Certificate Error on MacOS build ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi everyone, My package "ReactomeGSA" is currently not building on MacOS due to a presumably expired SSL certificate. The certificate was expired for a few days, but we renewed it already a few weeks ago. It seems, that the build system is not fetching the new certificate. On all other build systems, this was not an issue. Is there anything I can do to fix this? Thanks a lot for the help! Kind regards, Johannes ___ 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=IAwQeL3ZwYPC-UPj1PaXyO-ozUdzx6PzGvqZ5TFHL30=eRRX5w0jOGftTZq9BhefCu9wDIor4wPo6mpjAeVgt14= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ReactomeGSA - SSL Certificate Error on MacOS build
Hi everyone, My package "ReactomeGSA" is currently not building on MacOS due to a presumably expired SSL certificate. The certificate was expired for a few days, but we renewed it already a few weeks ago. It seems, that the build system is not fetching the new certificate. On all other build systems, this was not an issue. Is there anything I can do to fix this? Thanks a lot for the help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Git force push for scAnnotatR - Complete
Hi Nitesh, As we discussed, thanks a lot for doing the update on the Bioconductor Git server! Everything's working perfectly again. Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ReactomeGSA - Windows SSL error on tokay2
Hi, I'm getting a strange build error for the ReactomeGSA package. The package accesses our API through an https connection. I couldn't find any issue with our certificate. Builds on Linux and Mac are working fine. Therefore, it seems to be related to the certificate management on tokay2. I'd be grateful if you could let me know how I can further debug this issue. Our package also has the option to use non-encrypted http connections. If this is the only solution, could you maybe tell me how I can specifically change an option / parameter for only one of the build systems? Thanks for the help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
