[Bioc-devel] Macarron Next BiocRelease

2023-10-24 Thread sagun maharjan 
Hi Bioc Team,

We have fixed the windows build error for the Macarron package for the next
BioC release
https://bioconductor.org/checkResults/release/bioc-LATEST/Macarron/.

Are the next steps to push the Macarron github changes into the new BioC
release branch following the tutorial below?
https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories


Please suggest.

Regards,
Sagun

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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.

[Bioc-devel] RELEASE_3_18 branch is now available and push access is re-enabled

2023-10-24 Thread Kern, Lori via Bioc-devel 
Dear Maintainers,

You are now able to push your commits to the Bioconductor git server.

The RELEASE_3_18 branch is now available on Bioconductor. Please sync your
GitHub repositories with the latest updates to your package on Bioconductor for
a RELEASE_3_18 branch as well as the devel branch.

This link will get you going on how to Sync your GitHub repositories
https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories

Cheers,



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Is my package suitable for Bioconductor?

2023-10-24 Thread Kasper Daniel Hansen 
I am happy to talk on Zoom about this, since I have some interest in this
work.

Best,
Kasper

On Tue, Oct 24, 2023 at 9:21 AM Vincent Carey 
wrote:

> agreedthis discussion is best discussed in the open
>
> On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla 
> wrote:
>
> > Hi Tim,
> >
> > I think there is a mentorship program for cases like this (I am not sure
> if
> > it still accepts mentees):
> > https://www.bioconductor.org/developers/new-developer-program/
> > I also recommend the book the Bioconductor community wrote to help with
> > submissions: https://contributions.bioconductor.org/index.html
> >
> > Questions are usually posted here, which will not only help you but
> future
> > users/potential contributors with the same doubts/questions.
> > So I would recommend that if the previous resources do not help to just
> > list your questions here for anyone to chime in.
> >
> > If you want more feedback, you  may address the question to someone you
> > know from the community or using the slack to ask some questions are also
> > good options.
> >
> > Looking forward to seeing the package in Bioconductor.
> >
> > I hope this helps,
> >
> > Lluís
> >
> > On Tue, 24 Oct 2023 at 12:46, Timothy Barry 
> > wrote:
> >
> > > Hello,
> > >
> > > My collaborators and I are considering submitting our R package for
> > > single-cell CRISPR screen data analysis to Bioconductor (package
> website
> > <
> > > https://katsevich-lab.github.io/sceptre/> and e-book <
> > > https://timothy-barry.github.io/sceptre-book/>). We have several
> > > questions about the suitability of our package for Bioconductor and
> > changes
> > > that we might need to implement to make our package more consistent
> with
> > > Bioconductor package guidelines. Would a member of the Bioconductor
> team
> > be
> > > available for a brief (30-60 minute) Zoom call to discuss these issues?
> > We
> > > would very much appreciate the help.
> > >
> > > Thank you greatly,
> > > Tim Barry
> > >
> > > Timothy Barry, PhD
> > > University of Pennsylvania
> > > Department of Statistics and Data Science
> > > Postdoctoral researcher
> > >
> > >
> > > [[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
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:15}}

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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] Is my package suitable for Bioconductor?

2023-10-24 Thread Vincent Carey 
agreedthis discussion is best discussed in the open

On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla 
wrote:

> Hi Tim,
>
> I think there is a mentorship program for cases like this (I am not sure if
> it still accepts mentees):
> https://www.bioconductor.org/developers/new-developer-program/
> I also recommend the book the Bioconductor community wrote to help with
> submissions: https://contributions.bioconductor.org/index.html
>
> Questions are usually posted here, which will not only help you but future
> users/potential contributors with the same doubts/questions.
> So I would recommend that if the previous resources do not help to just
> list your questions here for anyone to chime in.
>
> If you want more feedback, you  may address the question to someone you
> know from the community or using the slack to ask some questions are also
> good options.
>
> Looking forward to seeing the package in Bioconductor.
>
> I hope this helps,
>
> Lluís
>
> On Tue, 24 Oct 2023 at 12:46, Timothy Barry 
> wrote:
>
> > Hello,
> >
> > My collaborators and I are considering submitting our R package for
> > single-cell CRISPR screen data analysis to Bioconductor (package website
> <
> > https://katsevich-lab.github.io/sceptre/> and e-book <
> > https://timothy-barry.github.io/sceptre-book/>). We have several
> > questions about the suitability of our package for Bioconductor and
> changes
> > that we might need to implement to make our package more consistent with
> > Bioconductor package guidelines. Would a member of the Bioconductor team
> be
> > available for a brief (30-60 minute) Zoom call to discuss these issues?
> We
> > would very much appreciate the help.
> >
> > Thank you greatly,
> > Tim Barry
> >
> > Timothy Barry, PhD
> > University of Pennsylvania
> > Department of Statistics and Data Science
> > Postdoctoral researcher
> >
> >
> > [[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
>

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Re: [Bioc-devel] Is my package suitable for Bioconductor?

2023-10-24 Thread Lluís Revilla 
Hi Tim,

I think there is a mentorship program for cases like this (I am not sure if
it still accepts mentees):
https://www.bioconductor.org/developers/new-developer-program/
I also recommend the book the Bioconductor community wrote to help with
submissions: https://contributions.bioconductor.org/index.html

Questions are usually posted here, which will not only help you but future
users/potential contributors with the same doubts/questions.
So I would recommend that if the previous resources do not help to just
list your questions here for anyone to chime in.

If you want more feedback, you  may address the question to someone you
know from the community or using the slack to ask some questions are also
good options.

Looking forward to seeing the package in Bioconductor.

I hope this helps,

Lluís

On Tue, 24 Oct 2023 at 12:46, Timothy Barry  wrote:

> Hello,
>
> My collaborators and I are considering submitting our R package for
> single-cell CRISPR screen data analysis to Bioconductor (package website <
> https://katsevich-lab.github.io/sceptre/> and e-book <
> https://timothy-barry.github.io/sceptre-book/>). We have several
> questions about the suitability of our package for Bioconductor and changes
> that we might need to implement to make our package more consistent with
> Bioconductor package guidelines. Would a member of the Bioconductor team be
> available for a brief (30-60 minute) Zoom call to discuss these issues? We
> would very much appreciate the help.
>
> Thank you greatly,
> Tim Barry
>
> Timothy Barry, PhD
> University of Pennsylvania
> Department of Statistics and Data Science
> Postdoctoral researcher
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Bioconductor Mirrors - Important Updates During Release Time

2023-10-24 Thread Kern, Lori via Bioc-devel 


For anyone that is maintaining a Bioconductor mirror/rsync please make any 
necessary updates within the next two weeks regarding location / legacy 
Bioconductor releases.

Starting last year, Bioconductor has moved archived versions of Bioconductor 
off the AWS cloudfront instance. Syncing to legacy releases of Bioconductor is 
not allowed and wasted effort as once Bioconductor freezes a release, no 
maintainer is allowed to make changes to that Bioconductor branch ever.  We 
would notify mirrors if any package has to be removed because of any violations 
and they would have to be removed manually.  Several of you have noticed this 
switch with Bioconductor versions <= 3.14.  Noticing that your rsync resulted 
in an empty repository.  In 2 weeks, November 8th we will begin the process of 
moving 3.17 off into the archive.  If you have set up your rsync to use 
numerical indications and/or with the --delete flag,  you may need to adjust 
your rsync commands to keep a legacy version of Bioconductor and not have it 
completely removed.  Please make any adjustment by November 8th.

https://bioconductor.org/about/mirrors/mirror-how-to/

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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[Bioc-devel] All commits to Bioconductor stopped from 8:00 am ET for release

2023-10-24 Thread Kern, Lori via Bioc-devel 
Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in
https://bioconductor.org/developers/release-schedule/

Today (October 24 th  2023) at 8:00 am ET, We will freeze the commits to all 
the branches and all packages in Bioconductor. We will notify here once we are 
done with the Release process and when commits can resume.

Once again, After 8:00 am today, you will temporarily not be able to push to 
the bioconductor git repo.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Is my package suitable for Bioconductor?

2023-10-24 Thread Timothy Barry 
Hello,

My collaborators and I are considering submitting our R package for single-cell 
CRISPR screen data analysis to Bioconductor (package website 
 and e-book 
). We have several questions 
about the suitability of our package for Bioconductor and changes that we might 
need to implement to make our package more consistent with Bioconductor package 
guidelines. Would a member of the Bioconductor team be available for a brief 
(30-60 minute) Zoom call to discuss these issues? We would very much appreciate 
the help.

Thank you greatly,
Tim Barry

Timothy Barry, PhD
University of Pennsylvania
Department of Statistics and Data Science
Postdoctoral researcher


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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]]

___
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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