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

[Andreas Tille]

Hi Nadiya,

thanks for your patience.  It seems we have spotted here a really buggy
package with missing dependencies.

On Mon, Mar 27, 2017 at 01:20:30PM -0700, Nadiya Sitdykova wrote:
> 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.

Do you want to say that after installing r-cran-rcppgsl on a clean
system is not able to run the test suite of r-cran-rcppgsl itself and
the installation of gsl-config is required to do so?

Or is it rather that gsl-config is required to run the test suite of
mapdamage?

> 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

Hmmm, at what point of the test is the linker ld called?
 
> So I also installed libopenblas-base and libopenblas-dev. NOW I got the
> same error as you.

I wonder in how far the development package is needed in the test suite.
May be it would be enlightening if you always would write down the
command you called and add a larger chunk of the resulting output.

As you describe things it seems this is another missing dependency.

> 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.

Would you mind reporting this in the upstream issue tracker?
 
Thanks for your patient work on this

       Andreas.

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