Outreachy 2017 (Round 14)

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Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello Andreas,

I am Busra from Turkey. I am studying Computer Engineering at Çanakkale 18 Mart University. I saw the Debian-Med idea at Outreachy organization's list and my friend Canberk told me about his experience on GSOC last year. I want to participate Outreachy so i am looking at bug 84326 . What should i do more for chosen.

Thanks for help. Regards.

Büşra Selin Pekişçi


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hello Büşra,

thanks for your interest in Debian Med.

On Thu, Mar 16, 2017 at 12:45:54AM +0300, Büşra Selin Pekişçi wrote:
> I am Busra from Turkey. I am studying Computer Engineering at Çanakkale 18
> Mart University. I saw the Debian-Med idea at Outreachy organization's list
> and my friend Canberk told me about his experience on GSOC last year.

Seems Canberk is spreading the Debian Med idea in Turkey. :-)

> I want to participate Outreachy so i am looking at bug 84326
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848326> . What should i
> do more for chosen.

Do you have some basic idea how to get the packaging VCS and the package
build process?  Is there any chance that Canberk gives you some quick
face to face introduction?  In any case I'd recommend to read the Debian
Med policy document[1] as a basic introduction into these questions.
Just feel free to ask here if anything might remain unclear.
 
> Thanks for help. Regards.

You are welcome

       Andreas.

[1] https://debian-med.alioth.debian.org/docs/policy.html

--
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Re: Outreachy 2017 (Round 14)

Nadiya Sitdykova
Hi all!

I've already been working on this bug for some time. Maybe it's ok if we both will work on it, but I decided just to notify if it's not ok.

On Wed, Mar 15, 2017 at 3:03 PM, Andreas Tille <[hidden email]> wrote:
Hello Büşra,

thanks for your interest in Debian Med.

On Thu, Mar 16, 2017 at 12:45:54AM +0300, Büşra Selin Pekişçi wrote:
> I am Busra from Turkey. I am studying Computer Engineering at Çanakkale 18
> Mart University. I saw the Debian-Med idea at Outreachy organization's list
> and my friend Canberk told me about his experience on GSOC last year.

Seems Canberk is spreading the Debian Med idea in Turkey. :-)

> I want to participate Outreachy so i am looking at bug 84326
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848326> . What should i
> do more for chosen.

Do you have some basic idea how to get the packaging VCS and the package
build process?  Is there any chance that Canberk gives you some quick
face to face introduction?  In any case I'd recommend to read the Debian
Med policy document[1] as a basic introduction into these questions.
Just feel free to ask here if anything might remain unclear.

> Thanks for help. Regards.

You are welcome

       Andreas.

[1] https://debian-med.alioth.debian.org/docs/policy.html

--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hi Nadiya,

On Wed, Mar 15, 2017 at 05:37:58PM -0700, Nadiya Sitdykova wrote:
> I've already been working on this bug for some time. Maybe it's ok if we
> both will work on it, but I decided just to notify if it's not ok.

Good point.   I forgot to check the numbers.  I guess its better if
everybody picks its own task since I do not see big potential for
sharing the worki in these issues.
 
Nadiya, if you have any questions please do not hesitate to ask here.

Kind regards

       Andreas.


--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello Again,

I pick this bug in a random way and did not see somebody working on it sorry. So i can take another bug :) I am reading the policy and keep in touch with Canberk .He mentioned me about alioth and packaging basics will help me on the progress.  Thanks for help

Regards

2017-03-16 10:02 GMT+03:00 Andreas Tille <[hidden email]>:
Hi Nadiya,

On Wed, Mar 15, 2017 at 05:37:58PM -0700, Nadiya Sitdykova wrote:
> I've already been working on this bug for some time. Maybe it's ok if we
> both will work on it, but I decided just to notify if it's not ok.

Good point.   I forgot to check the numbers.  I guess its better if
everybody picks its own task since I do not see big potential for
sharing the worki in these issues.

Nadiya, if you have any questions please do not hesitate to ask here.

Kind regards

       Andreas.


--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello All,

I made a testsuite for bug number #848329 . I look at program's website and there is no documentation so i made a simple test by looking examples. Now what should i do to commit code to you ? Thanks for help.

Regards

Büşra Selin Pekişçi



2017-03-16 12:20 GMT+03:00 Büşra Selin Pekişçi <[hidden email]>:
Hello Again,

I pick this bug in a random way and did not see somebody working on it sorry. So i can take another bug :) I am reading the policy and keep in touch with Canberk .He mentioned me about alioth and packaging basics will help me on the progress.  Thanks for help

Regards

2017-03-16 10:02 GMT+03:00 Andreas Tille <[hidden email]>:
Hi Nadiya,

On Wed, Mar 15, 2017 at 05:37:58PM -0700, Nadiya Sitdykova wrote:
> I've already been working on this bug for some time. Maybe it's ok if we
> both will work on it, but I decided just to notify if it's not ok.

Good point.   I forgot to check the numbers.  I guess its better if
everybody picks its own task since I do not see big potential for
sharing the worki in these issues.

Nadiya, if you have any questions please do not hesitate to ask here.

Kind regards

       Andreas.


--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-2
Hi Büşra

On Fri, Mar 17, 2017 at 11:21:44PM +0300, Büşra Selin Pekişçi wrote:
> I made a testsuite for bug number #848329
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848329> . I look at
> program's website and there is no documentation so i made a simple test by
> looking examples.

Sounds good.

> Now what should i do to commit code to you ? Thanks for
> help.

Did you created a login on alioth.debian.org as described in the Debian
Med policy?  If yes please either apply for the Debian Med team or let
me know your login name to make you a member of the team which will
grant you commit permissions to the Debian Med packaging repositories.

Then you can commit and I'll check your changes.

Thanks for your work on this

     Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello Andreas,

I make request to participate Debian-Med at Alioth fyi.

Best Regards.

2017-03-17 23:46 GMT+03:00 Andreas Tille <[hidden email]>:
Hi Büşra

On Fri, Mar 17, 2017 at 11:21:44PM +0300, Büşra Selin Pekişçi wrote:
> I made a testsuite for bug number #848329
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848329> . I look at
> program's website and there is no documentation so i made a simple test by
> looking examples.

Sounds good.

> Now what should i do to commit code to you ? Thanks for
> help.

Did you created a login on alioth.debian.org as described in the Debian
Med policy?  If yes please either apply for the Debian Med team or let
me know your login name to make you a member of the team which will
grant you commit permissions to the Debian Med packaging repositories.

Then you can commit and I'll check your changes.

Thanks for your work on this

     Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hi Büşra,

On Sun, Mar 19, 2017 at 10:29:01PM +0300, Büşra Selin Pekişçi wrote:
> I make request to participate Debian-Med at Alioth fyi.

I accepted yesterday evening - just let us know here if you have
problems commiting your changes.

Thanks for your work on this

      Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello Andreas,

I recognize Prank package at SVN i am not familiar with SVN what should i do ? Shall i look SVN or can somebody take package to Git. Thanks for help.

Best Regards.

2017-03-20 10:46 GMT+03:00 Andreas Tille <[hidden email]>:
Hi Büşra,

On Sun, Mar 19, 2017 at 10:29:01PM +0300, Büşra Selin Pekişçi wrote:
> I make request to participate Debian-Med at Alioth fyi.

I accepted yesterday evening - just let us know here if you have
problems commiting your changes.

Thanks for your work on this

      Andreas.

--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hi Büşra,

On Mon, Mar 20, 2017 at 11:36:32PM +0300, Büşra Selin Pekişçi wrote:
> I recognize Prank package at SVN i am not familiar with SVN what should i
> do ? Shall i look SVN or can somebody take package to Git. Thanks for help.

Since I have some experience with SVN to Git conversion I'll do so.

I'll ping here once this is done

     Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
On Tue, Mar 21, 2017 at 08:34:43AM +0100, Andreas Tille wrote:
> Since I have some experience with SVN to Git conversion I'll do so.
>
> I'll ping here once this is done

Prank is now at

    https://anonscm.debian.org/git/debian-med/prank.git

Have fun

     Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Büşra Selin Pekişçi
Hello Andreas,

I commit my work to git. Will move next bug . Thanks for help.

Best Regards

2017-03-21 11:01 GMT+03:00 Andreas Tille <[hidden email]>:
On Tue, Mar 21, 2017 at 08:34:43AM +0100, Andreas Tille wrote:
> Since I have some experience with SVN to Git conversion I'll do so.
>
> I'll ping here once this is done

Prank is now at

    https://anonscm.debian.org/git/debian-med/prank.git

Have fun

     Andreas.

--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hello Büşra,

On Thu, Mar 23, 2017 at 01:47:59AM +0300, Büşra Selin Pekişçi wrote:
> I commit my work to git. Will move next bug . Thanks for help.

Nice. :-)

I've added some further changes, mainly

  * Installing the test script into the package and a documentation
    for users how they can test the package themselves
  * Closing the bug inside the changelog

For everybody who intends to work on those tests:  Please make sure
you do the same in other packages.

Büşra, please inspect the changes I commited to learn what needs to
be done before a final upload.  I have also one remaining issue:

  Please document inside debian/README.source where you obtained
  the dataset from.

Thanks a lot for your work on this

      Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Nadiya Sitdykova
Hello, 

I've added tests of examples from here https://ginolhac.github.io/mapDamage/#a5 But only two of them works fine. Other two "Cannot use --<option> with missing R-libraries", so it seems they need recommended r-cran-rcppgsl package. I created simple stand-alone test with this package in depends to demonstrate that something goes wrong with installing RcppGSL. I looked at the source code here https://anonscm.debian.org/cgit/debian-med/mapdamage.git/tree/mapdamage/Rscripts/stats/checkLibraries.R and it looks like after package installation "library(RcppGSL)" doesn't load library correctly. I've been thinking about this problem for a while but didn't find solution yet. So I decided to commit working tests for now and ask for a help. Any thoughts?

On Thu, Mar 23, 2017 at 12:55 AM, Andreas Tille <[hidden email]> wrote:
Hello Büşra,

On Thu, Mar 23, 2017 at 01:47:59AM +0300, Büşra Selin Pekişçi wrote:
> I commit my work to git. Will move next bug . Thanks for help.

Nice. :-)

I've added some further changes, mainly

  * Installing the test script into the package and a documentation
    for users how they can test the package themselves
  * Closing the bug inside the changelog

For everybody who intends to work on those tests:  Please make sure
you do the same in other packages.

Büşra, please inspect the changes I commited to learn what needs to
be done before a final upload.  I have also one remaining issue:

  Please document inside debian/README.source where you obtained
  the dataset from.

Thanks a lot for your work on this

      Andreas.

--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hi Nadiya,

thanks for your work on this.  It seems you've hit a non-trival example
but that's no problem but rather a challenge, right?

At first I've fixed debian/changelog.  It seems you always called

    dch -i

which is for each call bumping the Debian release.  Please use the -i
option only once.  Even better use

    dch --team

since this adds the "Team upload" entry which marks the upload in a way
that lintian (the Debian policy checker) does not claim that the
changelog owner is not listed as Uploader in debian/control.

Please git pull to see the result.

On Thu, Mar 23, 2017 at 09:55:37PM -0700, Nadiya Sitdykova wrote:
> I've added tests of examples from here
> https://ginolhac.github.io/mapDamage/#a5 But only two of them works fine.

Hmm, I admit I get a strange error even here:

mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa
Started with the command: /usr/bin/mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa
        Reading from 'rescale_test/pe_test/pe.sam'
        Writing results to 'results_pe/'
pdf results_pe/Fragmisincorporation_plot.pdf generated
No length distributions are available, plotting length distribution only works for single-end reads
Error: Seqtk failed: [Errno 2] No such file or directory

I applied all patches via

   quilt push -a

and checked for occurences of seqtk via:

mapdamage(master) $ grep -Riw Seqtk | grep -v -e "^\." -e "^debian"
mapdamage/composition.py:    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk")
mapdamage/composition.py:        sys.stderr.write("Error: Seqtk failed: %s\n" % (error,))
bin/mapDamage:    fpath_seqtk = '/usr/bin/seqtk'
bin/mapDamage:        sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"

So it seems that in mapdamage/composition.py the path to seqtk is not
properly assembled.  Would you mind checking this?

> Other two "Cannot use --<option> with missing R-libraries", so it seems
> they need recommended r-cran-rcppgsl package. I created simple stand-alone
> test with this package in depends to demonstrate that something goes wrong
> with installing RcppGSL. I looked at the source code here
> https://anonscm.debian.org/cgit/debian-med/mapdamage.git/tree/mapdamage/Rscripts/stats/checkLibraries.R
> and
> it looks like after package installation "library(RcppGSL)" doesn't load
> library correctly.

Hmmm, GSL rings a bell for me.  There was a gsl library transistion.
Are you using a current Debian testing or unstable system?  If not that
might be the cause of the issue.  May be you explain more verbosely
what exactly you mean by "doesn't load library correctly"?
 
I get

$ mapDamage --check-R-packages
All R packages are present


After checking mapdamage/rscript.py what R packages are really checked I
added some R packages as real Depends.  I personally follow the strategy
to use Depends if a package is needed to run the full test suite.  While
I actually learned from your commits that you can work around this via
"needs-recommends" (its nice to learn when mentoring ;-) ) I'm sure
users really want to have the full functionality.

In summary please do the following:

  1. Check why seqtk is not found in mapdamage/composition.py
     my guess is that the current quilt patch is incomplete.

  2. If the R test keeps on failing please provide more information

Thanks again for your work on this

     Andreas.

PS: Regarding the time delay you mentioned in your other mail:  That's
    fine - we have team members in different time zones. :-)

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Nadiya Sitdykova
Hello Andreas,

Thank you for instructions for using dch, I hope now I got it right.

1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem with seqtk should be resolved now. 

2) I have this error on Ubuntu xenial, Debian jessie and after you mentioned that it's better to use unstable version, I tried Debian sid (amd64) and still got problems with RcppGSL.
That stand-alone test returns exit code 1 with message "Missing the following R library RcppGSL". And for commented tests in run-unit-test file the message is "Cannot use --stats-only with missing R libraries".

Regards, Nadiya



On Fri, Mar 24, 2017 at 3:32 AM, Andreas Tille <[hidden email]> wrote:
Hi Nadiya,

thanks for your work on this.  It seems you've hit a non-trival example
but that's no problem but rather a challenge, right?

At first I've fixed debian/changelog.  It seems you always called

    dch -i

which is for each call bumping the Debian release.  Please use the -i
option only once.  Even better use

    dch --team

since this adds the "Team upload" entry which marks the upload in a way
that lintian (the Debian policy checker) does not claim that the
changelog owner is not listed as Uploader in debian/control.

Please git pull to see the result.

On Thu, Mar 23, 2017 at 09:55:37PM -0700, Nadiya Sitdykova wrote:
> I've added tests of examples from here
> https://ginolhac.github.io/mapDamage/#a5 But only two of them works fine.

Hmm, I admit I get a strange error even here:

mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa
Started with the command: /usr/bin/mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa
        Reading from 'rescale_test/pe_test/pe.sam'
        Writing results to 'results_pe/'
pdf results_pe/Fragmisincorporation_plot.pdf generated
No length distributions are available, plotting length distribution only works for single-end reads
Error: Seqtk failed: [Errno 2] No such file or directory

I applied all patches via

   quilt push -a

and checked for occurences of seqtk via:

mapdamage(master) $ grep -Riw Seqtk | grep -v -e "^\." -e "^debian"
mapdamage/composition.py:    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk")
mapdamage/composition.py:        sys.stderr.write("Error: Seqtk failed: %s\n" % (error,))
bin/mapDamage:    fpath_seqtk = '/usr/bin/seqtk'
bin/mapDamage:        sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"

So it seems that in mapdamage/composition.py the path to seqtk is not
properly assembled.  Would you mind checking this?

> Other two "Cannot use --<option> with missing R-libraries", so it seems
> they need recommended r-cran-rcppgsl package. I created simple stand-alone
> test with this package in depends to demonstrate that something goes wrong
> with installing RcppGSL. I looked at the source code here
> https://anonscm.debian.org/cgit/debian-med/mapdamage.git/tree/mapdamage/Rscripts/stats/checkLibraries.R
> and
> it looks like after package installation "library(RcppGSL)" doesn't load
> library correctly.

Hmmm, GSL rings a bell for me.  There was a gsl library transistion.
Are you using a current Debian testing or unstable system?  If not that
might be the cause of the issue.  May be you explain more verbosely
what exactly you mean by "doesn't load library correctly"?

I get

$ mapDamage --check-R-packages
All R packages are present


After checking mapdamage/rscript.py what R packages are really checked I
added some R packages as real Depends.  I personally follow the strategy
to use Depends if a package is needed to run the full test suite.  While
I actually learned from your commits that you can work around this via
"needs-recommends" (its nice to learn when mentoring ;-) ) I'm sure
users really want to have the full functionality.

In summary please do the following:

  1. Check why seqtk is not found in mapdamage/composition.py
     my guess is that the current quilt patch is incomplete.

  2. If the R test keeps on failing please provide more information

Thanks again for your work on this

     Andreas.

PS: Regarding the time delay you mentioned in your other mail:  That's
    fine - we have team members in different time zones. :-)

--
http://fam-tille.de


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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hello Nadiya,

On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote:
> Thank you for instructions for using dch, I hope now I got it right.

I think so (except the blank line in the beginning which was probably
a typo).
 
> 1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem
> with seqtk should be resolved now.

Yes, this works now for me.
 
> 2) I have this error on Ubuntu xenial, Debian jessie and after you
> mentioned that it's better to use unstable version, I tried Debian sid
> (amd64) and still got problems with RcppGSL.
> That stand-alone test returns exit code 1 with message "Missing the
> following R library RcppGSL".

This is very strange.  I can confirm that there is really a problem
if I run

 LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out

I get the attached build log - but this does not contain the string
Rcpp.  This needs to be investigated.

> And for commented tests in run-unit-test file
> the message is "Cannot use --stats-only with missing R libraries".

I think it would be the best to stick to the not commented tests
and make sure we get the same results.  Could you please also
create the exact output if your test?

Kind regards

        Andreas.

--
http://fam-tille.de

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Re: Outreachy 2017 (Round 14)

Nadiya Sitdykova
Hello Andreas,

I generated output files for run-unit-test and run-r-packages-check the exact same way you described. 

Regards, Nadiya

On Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille <[hidden email]> wrote:
Hello Nadiya,

On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote:
> Thank you for instructions for using dch, I hope now I got it right.

I think so (except the blank line in the beginning which was probably
a typo).

> 1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem
> with seqtk should be resolved now.

Yes, this works now for me.

> 2) I have this error on Ubuntu xenial, Debian jessie and after you
> mentioned that it's better to use unstable version, I tried Debian sid
> (amd64) and still got problems with RcppGSL.
> That stand-alone test returns exit code 1 with message "Missing the
> following R library RcppGSL".

This is very strange.  I can confirm that there is really a problem
if I run

 LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out

I get the attached build log - but this does not contain the string
Rcpp.  This needs to be investigated.

> And for commented tests in run-unit-test file
> the message is "Cannot use --stats-only with missing R libraries".

I think it would be the best to stick to the not commented tests
and make sure we get the same results.  Could you please also
create the exact output if your test?

Kind regards

        Andreas.

--
http://fam-tille.de


run-unit-test.out (2K) Download Attachment
run-r-package-check.out (56 bytes) Download Attachment
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Re: Outreachy 2017 (Round 14)

Andreas Tille-5
Hi Nadiya,

On Sun, Mar 26, 2017 at 02:31:47PM -0700, Nadiya Sitdykova wrote:
> I generated output files for run-unit-test and run-r-packages-check the
> exact same way you described.

Regarding run-r-package-check.out.  Could you please post the result of

  apt-cache policy r-cran-rcppgsl


> On Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille <[hidden email]> wrote:
> >
> >  LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
> >
> > I get the attached build log - but this does not contain the string
> > Rcpp.  This needs to be investigated.

It really seems that your r-cran-rcppgsl installation is broken.  You
might like to try

  apt-get source r-cran-rcppgsl
  LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R

to make sure this R module works properly.  I admit I have not
experienced severy problems with R modules on clean Debian systems.

Once we get r-cran-rcppgsl working properly you will probably get the
same errors as I observed.

Kind regards

      Andreas.

--
http://fam-tille.de

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