Hervé, Martin, Thank you so much, atena builds and checks cleanly now on kunpeng2 too!!
https://bioconductor.org/checkResults/3.18/bioc-LATEST/atena cheers, robert. On 10/23/23 20:46, Hervé Pagès wrote: > > 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 | 100000 | 2.16 / 20 >> o template has single segment.... S | 0 | 0 | NA / NA >> o template has multiple segments. M | 215602 | 100000 | 2.16 / 20 >> - first segment.............. F | 107801 | 100000 | 1.08 / 10 >> - last segment............... L | 107801 | 100000 | 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 | 100000 | 2.16 / 20 >> - primary alignment......... M2 | 200000 | 100000 | 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 | 100000 | 1.08 / 10 >> - primary alignment......... F2 | 100000 | 100000 | 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 | 100000 | 1.08 / 10 >> - primary alignment......... L2 | 100000 | 100000 | 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 >> <hpages.on.git...@gmail.com> 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 -- 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
