1) Yes, I mean after I tried apt-get source r-cran-rcppgsl LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R
There was an error "gsl-config not found". Unfortunately, I didn't save that log and can't reproduce it now =( 2) I executed autopkgtest . -- null and run-unit-test failed after linker call, I saved that log so it's attached 3) Done On Mon, Mar 27, 2017 at 2:03 PM, Andreas Tille <andr...@an3as.eu> wrote: > 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. > > -- > http://fam-tille.de > >
run-unit-test.out
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