Hi again, I solved this by simply removing the whole configure script in a quilt patch.
Kind regards Andreas. On Mon, May 09, 2016 at 05:01:52PM +0200, Andreas Tille wrote: > 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/ > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de