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16 Mar 2009


      Dear list,
Once again I come here to ask for your help/opinion :-)
I have decided to give some more love to two of my packages:
R-BSgenome.Dmelanogaster.FlyBase.r51 and R-BSgenome.Celegans.UCSC.ce2
In order to be able to build the latest versions of them I need to
package the following:
R-IRange R-Biostrings and R-BSgenome
So I did and before submitting them for review, I would like to expose
here the problem I have with them.
While packaging R-IRange has obtain:
R-IRanges.x86_64: W:
devel-file-in-non-devel-package /usr/lib64/R/library/IRanges/include/...
So I divided the package in a sub package -devel with the following
error:
R-IRanges-devel.x86_64: E: only-non-binary-in-usr-lib
while all the package is in %{_libdir}
If I move the headers from %{_libdir} to %{_datadir} as rpmlint ask then
I have to do the following in R-Biostrings spec:
---------------SPEC
# Replace the wrong include by the rights one :)
for i in %{packname}/src/*.c
 do 
   sed -i -e 's|#include "IRanges_interface.h"| #include
"%{_datadir}/R/library/IRanges/include/include/IRanges_interface.h"|' $i
 done
sed -i -e 's|#include "IRanges_defines.h"| #include
"%{_datadir}/R/library/IRanges/include/include/IRanges_defines.h"|'
%{packname}/inst/include/Biostrings_de
fines.h
sed -i -e 's|#include "_IRanges_stubs.c"| #include
"%{_datadir}/R/library/IRanges/include/include/_IRanges_stubs.c"|'
%{packname}/src/IRanges_stubs.c
-----------------EOF
Because else Biostrings cannot find the correct headers and thus cannot
compile...
And... R-Biostrings needs also to be split in a subpackage -devel with
the headers in %{_libdir} while the package is installed in %{_datadir}
so R-BSgenome will also have to be "patched" for the headers.
Is there a way to make R looking in both %{_datadir} and %{_libdir}
while it looks for the headers ?
Could I leave the R headers in %{_libdir} ? (I guess not but worth to
ask ^^)
Any suggestion/remarks ?
Thanks in advance,
Best regards,
Pierre