[Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

[Martin Grigorov]

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 ?

Regards,
Martin


On Mon, Oct 23, 2023 at 7:26 PM Hervé Pagès <hpages.on.github using 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.github using gmail.com
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]