[Debian-med-packaging] Bug#848326: Outreachy 2017 (Round 14)

[Nadiya Sitdykova]

Here is the output of apt-cache policy r-cran-rcppgsl:

r-cran-rcppgsl:
  Installed: 0.3.2-1
  Candidate: 0.3.2-1
  Version table:
 *** 0.3.2-1 500
        500 http://ftp.us.debian.org/debian sid/main amd64 Packages
        100 /var/lib/dpkg/status

tests for r-cran-rcppgsl crashed because of absence of gsl-config. So I've
done some googling, installed gsl-devel and it helped with
run-r-packages-check but I still didn't get the same error for
run-unit-test as you, I got:

    Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
cannot find -llapack
/usr/bin/ld: cannot find -lblas

So I also installed libopenblas-base and libopenblas-dev. NOW I got the
same error as you. I looked into it, and it seems that the problem is that
in the test data nucleotide frequency array looks like 0.5555556 0.2222222
0.2222222 0,
i.e. frequence for T is zero, which is not what expected by mapdamage from
line 4 in
https://github.com/ginolhac/mapDamage/blob/master/mapdamage/Rscripts/stats/function.R#L4
Even though documentation doesn't say that zero frequences are not allowed.

I changed reference file from "CGAGGGCGA" to "TGAAAACGA" (so all frequences
> 0) and now it executes without errors.

Regards, Nadiya

On Sun, Mar 26, 2017 at 11:40 PM, Andreas Tille <andreas at an3as.eu> wrote:

> 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 <andreas at an3as.eu> 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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