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

Robert Castelo robert@c@@te|o @end|ng |rom up|@edu
Tue Oct 24 19:16:22 CEST 2023


oops, sorry, indeed, the question was about the gDNAx package and now 
it's all green, including kunpeng2, thank you!!

robert.

On 10/24/23 15:52, Hervé Pagès wrote:
>
> 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

-- 
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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