[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 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
> 
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