Unittest of oligoClasses tries to write data to /usr/local/lib/R/site-library
Hi,
the Debian R packaging team has created Debian packages of oligoClasses.
When running the test suite I get:
...
Executing test function test_CopyNumberSet_construction ... Loading required package: pd.mapping50k.hind240
Attempting to obtain 'pd.mapping50k.hind240' from BioConductor website.
Checking to see if your internet connection works...
You do not have write access to '/usr/local/lib/R/site-library'.
Timing stopped at: 0.077 0.019 0.899
Error in get(annotation) : object 'pd.mapping50k.hind240' not found
done successfully.
Executing test function test_dataExamples ... done successfully.
Executing test function test_GenomeAnnotatedDataFrame_construction ... Loading required package: pd.mapping50k.hind240
done successfully.
Executing test function test_GenomeAnnotatedDataFrameWithFF ... Loading required package: pd.mapping50k.hind240
Attempting to obtain 'pd.mapping50k.hind240' from BioConductor website.
Checking to see if your internet connection works...
You do not have write access to '/usr/local/lib/R/site-library'.
Timing stopped at: 0.148 0.001 0.566
Error in get(annotation) : object 'pd.mapping50k.hind240' not found
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.mapping50k.hind240’
done successfully.
Executing test function test_oligoSnpSet_construction ... Loading required package: pd.mapping50k.hind240
...
When running the test as root it passes successfully but I think
tests should not touch /usr in general.
Kind regards
Andreas.
--
http://fam-tille.de
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