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

[Hervé Pagès]

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.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
>
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>
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>     Bioc-devel using r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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