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

[Robert Castelo]

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.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
>>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using 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

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