oops, sorry, indeed, the question was about the gDNAx package and now it's all green, including kunpeng2, thank you!!
robert. On 10/24/23 15:52, Hervé Pagès wrote: > > That was actually about the gDNAx package (based on the URL you > provided in your original post), which will hopefully turn green on > kunpeng2 today: > https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx > > Best, > > H. > > On 10/23/23 23:29, Robert Castelo wrote: >> >> 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 > -- > 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
