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

[Hervé Pagès]

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.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

-- 
Hervé Pagès

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

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