[Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

[Andreas Tille]

Hi,

usually R packages are building without problems but I faced an issue
now which I have no clue about.  I try to upgrade r-bioc-rtracklayer[1]
and I have updated SVN to something that should build version 1.32.0.

Unfortunately when using pbuilder I get:

dh_testroot
dh_prep 
dh_installdirs -A 
mkdir -p "."
dh_installdirs          usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.3.0-1), r-api-3" >> debian/r-bioc-rtracklayer.substvars
if test -f /usr/bin/xvfb-run; then                      \
                 xvfb-run -a                    \
                        R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean     \
                                 .      \
                                "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\""                 \
                                ;                               \
        else                                                    \
                 R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library     \
                                --clean  .  \
                                "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\""                 \
                                ;                               \
        fi
* installing *source* package 'rtracklayer' ...
configure: error: cannot find sources (rtracklayer) in . or ..
ERROR: configuration failed for package 'rtracklayer'
* removing '/build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer'
/usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
make: *** [R_any_arch] Error 1
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2


The issue is that the configure scripts seeks a dir rtracklayer either
in . or .. but pbuilder renames the build directory to
r-bioc-rtracklayer-1.32.0.  The package builds fine with debuild.

This is the first time I'm observing and I wonder whether there is a
better way to fix this than patching the configure script.
Unfortunately I'm not that comfortable with cdbs hooks to know how to
possibly set a symlink to the proper dir in advance or something like
this.

Any help would be welcome

       Andreas.

[1] svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/

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