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