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

2023-10-24 Thread Robert Castelo 
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 | 10 | 2.16 / 20
   o template has single segment S |        0 |  0 |   NA / NA
   o template has multiple segments. M |   215602 | 10 | 2.16 / 20
       - first segment.. F |   107801 | 10 | 1.08 / 10
       - last segment... L |   107801 | 10 | 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 | 10 | 2.16 / 20
       - primary alignment. M2 |   20 | 10 |    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 | 10 | 1.08 / 10
       - primary alignment. F2 |   10 | 10 |    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 | 10 | 1.08 / 10
       - primary alignment. L2 |   10 | 10 |    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 
  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.

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

2023-10-24 Thread 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 | 10 | 2.16 / 20
>>>   o template has single segment S |        0 |  0 |   NA / NA
>>>   o template has multiple segments. M |   215602 | 10 | 2.16 / 20
>>>       - first segment.. F |   107801 | 10 | 1.08 / 10
>>>       - last segment... L |   107801 | 10 | 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 | 10 | 2.16 / 20
>>>       - primary alignment. M2 |   20 | 10 |    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 | 10 | 1.08 / 10
>>>       - primary alignment. F2 |   10 | 10 |    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 | 10 | 1.08 / 10
>>>       - primary alignment. L2 |   10 | 10 |    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 
>>>  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:
>>> >
>>> >
>>> 
>>>

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

2023-10-24 Thread Martin Grigorov 
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 |   10 | 2.16 / 20
  o template has single segment S |0 |0 |   NA / NA
  o template has multiple segments. M |   215602 |   10 | 2.16 / 20
  - first segment.. F |   107801 |   10 | 1.08 / 10
  - last segment... L |   107801 |   10 | 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 |   10 | 2.16 / 20
  - primary alignment. M2 |   20 |   10 |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 |   10 | 1.08 / 10
  - primary alignment. F2 |   10 |   10 |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 |   10 | 1.08 / 10
  - primary alignment. L2 |   10 |   10 |1 / 1
  - secondary alignment... L3 | 7801 | 4085 | 1.91 / 9
  o record is unmapped L4 |0 |0 |   NA / NA


Looks good ?

Regards,
Martin


On Mon, Oct 23, 2023 at 7:26 PM Hervé Pagès 
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.git...@gmail.com
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2023-10-24 Thread 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 |   10 | 2.16 / 20
>>   o template has single segment S |        0 |        0 |   NA / NA
>>   o template has multiple segments. M |   215602 |   10 | 2.16 / 20
>>       - first segment.. F |   107801 |   10 | 1.08 / 10
>>       - last segment... L |   107801 |   10 | 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 |   10 | 2.16 / 20
>>       - primary alignment. M2 |   20 |   10 |    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 |   10 | 1.08 / 10
>>       - primary alignment. F2 |   10 |   10 |    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 |   10 | 1.08 / 10
>>       - primary alignment. L2 |   10 |   10 |    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 
>>  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

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

2023-10-23 Thread 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 |   10 | 2.16 / 20
>   o template has single segment S |        0 |        0 |   NA / NA
>   o template has multiple segments. M |   215602 |   10 | 2.16 / 20
>       - first segment.. F |   107801 |   10 | 1.08 / 10
>       - last segment... L |   107801 |   10 | 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 |   10 | 2.16 / 20
>       - primary alignment. M2 |   20 |   10 |    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 |   10 | 1.08 / 10
>       - primary alignment. F2 |   10 |   10 |    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 |   10 | 1.08 / 10
>       - primary alignment. L2 |   10 |   10 |    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 
>  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.git...@gmail.com
>
>         [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

[[alternative HTML version deleted]]

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

2023-10-23 Thread Hervé Pagès 
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.git...@gmail.com

[[alternative HTML version deleted]]

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

2023-10-23 Thread Robert Castelo 

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.

--
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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