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 <andr...@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 <andr...@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 > >