[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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