Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64
On 10/23/23 11:45, Martin Grigorov wrote:
> Hi,
>
> > quickBamFlagSummary(eh[["EH8081"]])
> see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
> documentation
> loading from cache
> [E::hts_hopen] Failed to open file
> /home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133
> [E::hts_open_format] Failed to open file
> "/home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133" : Exec
> format error
> Error in value[[3L]](cond) :
> failed to open BamFile: failed to open SAM/BAM file
> file: '/home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133'
> > eh[["EH8081", force=TRUE]]
> see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
> documentation
> downloading 2 resources
> retrieving 2 resources
> |==|
> 100%
>
> |==|
> 100%
>
> loading from cache
> class: BamFile
> path: /home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133
> index: /home/biocbuild/.cache/R/ExperimentHub/1d1f2d19075fb4_8134
> isOpen: FALSE
> yieldSize: NA
> obeyQname: FALSE
> asMates: FALSE
> qnamePrefixEnd: NA
> qnameSuffixStart: NA
> > quickBamFlagSummary(eh[["EH8081"]])
> see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
> documentation
> loading from cache
> [E::idx_find_and_load] Could not retrieve index file for
> '/home/biocbuild/.cache/R/ExperimentHub/1d1f2d19075fb4_8134'
> group | nb of | nb of | mean / max
> of | records | unique | records per
> records | in group | QNAMEs | unique QNAME
> All records A | 215602 | 10 | 2.16 / 20
> o template has single segment S | 0 | 0 | NA / NA
> o template has multiple segments. M | 215602 | 10 | 2.16 / 20
> - first segment.. F | 107801 | 10 | 1.08 / 10
> - last segment... L | 107801 | 10 | 1.08 / 10
> - other segment.. O | 0 | 0 | NA / NA
>
> Note that (S, M) is a partitioning of A, and (F, L, O) is a
> partitioning of M.
> Indentation reflects this.
>
> Details for group M:
> o record is mapped.. M1 | 215602 | 10 | 2.16 / 20
> - primary alignment. M2 | 20 | 10 | 2 / 2
> - secondary alignment... M3 | 15602 | 4085 | 3.82 / 18
> o record is unmapped M4 | 0 | 0 | NA / NA
>
> Details for group F:
> o record is mapped.. F1 | 107801 | 10 | 1.08 / 10
> - primary alignment. F2 | 10 | 10 | 1 / 1
> - secondary alignment... F3 | 7801 | 4085 | 1.91 / 9
> o record is unmapped F4 | 0 | 0 | NA / NA
>
> Details for group L:
> o record is mapped.. L1 | 107801 | 10 | 1.08 / 10
> - primary alignment. L2 | 10 | 10 | 1 / 1
> - secondary alignment... L3 | 7801 | 4085 | 1.91 / 9
> o record is unmapped L4 | 0 | 0 | NA / NA
>
>
> Looks good ?
Looks good. Thanks Martin!
H.
>
> Regards,
> Martin
>
>
> On Mon, Oct 23, 2023 at 7:26 PM Hervé Pagès
> wrote:
>
> Hi Robert,
>
> There's the possibility that some of these BAM files got corrupted
> when
> downloaded to kunpeng2 local cache.
>
> @Martin Gregorov: Would you be able to try to run the following on
> kunpeng2?
>
> library(Rsamtools)
> library(ExperimentHub)
> eh <- ExperimentHub()
> quickBamFlagSummary(eh[["EH8081"]])
>
> If you get an error that the file cannot be opened, then maybe try to
> re-download it with:
>
> eh[["EH8081", force=TRUE]]
>
> Then try quickBamFlagSummary(eh[["EH8081"]]) again and hopefully
> it will
> work.
>
> Thanks,
>
> H.
>
> On 10/23/23 08:03, Robert Castelo wrote:
> > hi,
> >
> > our package atena fails to build **only** in kunpeng2 Linux
> openEuler
> > 22.03 LTS-SP1 / aarch64:
> >
> >
>
> https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx/kunpeng2-buildsrc.html
>
> >
> >
> > concretely, the vignette fails to find a BAM file downloaded via
> > ExperimentHub. This does not happen in any of the other platforms.
> > Should we do anything about this?
> >
> > Thanks!
> >
> > robert.
> >
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
> [[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
[[alternative HTML version deleted]]
Re: [Bioc-devel] Build error on nebbiolo2
Hi Gregory, Looks like GDAL is missing on nebbolo2. We're looking into this. Thanks for letting us know, H. On 10/23/23 10:25, Gregory B. Gloor wrote: > Hello, > > I received an error today on this machine for ALDEx2 > > I last committed 12 days ago and until today it was building cleanly on > everything. I am not sure what I can do to fix the error since I don't know > what dependency is calling that library file > > Any help appreciated > > Greg > > ## > ## > ### > ### Running command: > ### > ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs > --no-resave-data ALDEx2 > ### > ## > ## > > > * checking for file ‘ALDEx2/DESCRIPTION’ ... OK > * preparing ‘ALDEx2’: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > --- re-building ‘ALDEx2_vignette.Rmd’ using rmarkdown > --- finished re-building ‘ALDEx2_vignette.Rmd’ > > --- re-building ‘scaleSim_vignette.Rmd’ using rmarkdown > > Quitting from lines 331-419 [graph] (scaleSim_vignette.Rmd) > Error: processing vignette 'scaleSim_vignette.Rmd' failed with diagnostics: > unable to load shared object > '/home/biocbuild/bbs-3.18-bioc/R/site-library/sf/libs/sf.so': > libgdal.so.30: cannot open shared object file: No such file or directory > --- failed re-building ‘scaleSim_vignette.Rmd’ > > SUMMARY: processing the following file failed: > ‘scaleSim_vignette.Rmd’ > > Error: Vignette re-building failed. > Execution halted > ___ > 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Build error on nebbiolo2
Hello, I received an error today on this machine for ALDEx2 I last committed 12 days ago and until today it was building cleanly on everything. I am not sure what I can do to fix the error since I don't know what dependency is calling that library file Any help appreciated Greg ## ## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ALDEx2 ### ## ## * checking for file ‘ALDEx2/DESCRIPTION’ ... OK * preparing ‘ALDEx2’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘ALDEx2_vignette.Rmd’ using rmarkdown --- finished re-building ‘ALDEx2_vignette.Rmd’ --- re-building ‘scaleSim_vignette.Rmd’ using rmarkdown Quitting from lines 331-419 [graph] (scaleSim_vignette.Rmd) Error: processing vignette 'scaleSim_vignette.Rmd' failed with diagnostics: unable to load shared object '/home/biocbuild/bbs-3.18-bioc/R/site-library/sf/libs/sf.so': libgdal.so.30: cannot open shared object file: No such file or directory --- failed re-building ‘scaleSim_vignette.Rmd’ SUMMARY: processing the following file failed: ‘scaleSim_vignette.Rmd’ Error: Vignette re-building failed. Execution halted ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64
Hi Robert, There's the possibility that some of these BAM files got corrupted when downloaded to kunpeng2 local cache. @Martin Gregorov: Would you be able to try to run the following on kunpeng2? library(Rsamtools) library(ExperimentHub) eh <- ExperimentHub() quickBamFlagSummary(eh[["EH8081"]]) If you get an error that the file cannot be opened, then maybe try to re-download it with: eh[["EH8081", force=TRUE]] Then try quickBamFlagSummary(eh[["EH8081"]]) again and hopefully it will work. Thanks, H. On 10/23/23 08:03, Robert Castelo wrote: > hi, > > our package atena fails to build **only** in kunpeng2 Linux openEuler > 22.03 LTS-SP1 / aarch64: > > https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx/kunpeng2-buildsrc.html > > > > concretely, the vignette fails to find a BAM file downloaded via > ExperimentHub. This does not happen in any of the other platforms. > Should we do anything about this? > > Thanks! > > robert. > -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64
hi, our package atena fails to build **only** in kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64: https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx/kunpeng2-buildsrc.html concretely, the vignette fails to find a BAM file downloaded via ExperimentHub. This does not happen in any of the other platforms. Should we do anything about this? Thanks! robert. -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.18
Hello Bioconductor developers, We are still on track for Bioconductor Release 3.18 for this Wednesday October 25th. This means that tonight is the last day to commit changes to the devel branch before creation of the RELEASE_3_18 versions of your packages. And any changes you make to your packages at this point will not be reflected in a build report before we branch. There will be a temporary code freeze tomorrow morning (EST) while the branching for RELEASE_3_18 occurs automatically by the core team. You will receive emails when the freeze occurs and when commits to the branches can resume. As clarification, you will still be able to commit to the release 3.18 branch and the devel branch throughout the next release cycle. But any packages that have not been fixed for failures or bugs in devel would then have to be fixed/uploaded to both the RELEASE_3_18 branch and the devel branch after tomorrow morning. Any package that remains broken in release would also be candidates for deprecation in 3.19 Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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
