Re: Outreachy 2017 (Round 14)

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@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@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.

--
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