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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel