Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)
Hi Dirk, On Mon, May 09, 2016 at 02:37:37PM -0500, Dirk Eddelbuettel wrote: > > Sorry, meant whichever version (of rtracklayer) gave you that issue. I would > rather not remove configure wholesale. > > I am reasonably fluent at writing these so I may be able to help you just > modify the existing one by taking the offending test out Hmmm, its no problem to kick out the relevant test (I managed on my local disk successfully). But are you *really* sure that editing autogenerated files that are actually not supposed to be edited manually but under control of autoconf is the best solution for the problem? I never ever had the need to edit a configure file and if there was ever any need to fix a broken one using dh-autoreconf was the working solution. Moreover I noticed that after *removing* configure the option -DUSE_SSL was used while when I just skipped the test inside the configure file it was *not* included which seems like the configure file is broken in several ways. So it sounds reasonable to me to stick to my initial strategy and to assume that the configure file was delivered by accident and thus removing it. Kind regards Andreas. -- http://fam-tille.de
Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)
On 9 May 2016 at 21:10, Andreas Tille wrote: | > Or rather, I take the 'self-directory' | > test out in 3.2. | | You probably mean 3.3, right? Version 3.2 has no such test as far as I | can see. Sorry, meant whichever version (of rtracklayer) gave you that issue. I would rather not remove configure wholesale. I am reasonably fluent at writing these so I may be able to help you just modify the existing one by taking the offending test out, but I'm at work now so ... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)
Hi Dirk, On Mon, May 09, 2016 at 01:55:42PM -0500, Dirk Eddelbuettel wrote: > > On 9 May 2016 at 20:37, Andreas Tille wrote: > | Hi again, > | > | I solved this by simply removing the whole configure script in a quilt > patch. > > That sounds crazy so I took a look. BioConductor just had a 3.3 release > (matching the R release cycle) and they seemingly simplified it a lot. > Compare these two: > > https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.2/configure.ac > > https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.3/configure.ac I can confirm that I did compared the old and the new release. Since the old release did not had a configure script (*without* the .ac!) in its release tarball I came to the conclusion that this might be unneeded and in fact it is. My guess is that it will be recreated from configure.ac (as it should be). > I did not look too closely at the older one but the newer does check for > OpenSSL present or not __and then uses this in src/Makevars.in__ so if it > were me I consider switching to this. I can confirm that I also added Build-Depends: libssl-dev. > Or rather, I take the 'self-directory' > test out in 3.2. You probably mean 3.3, right? Version 3.2 has no such test as far as I can see. Kind regards Andreas. -- http://fam-tille.de
Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)
On 9 May 2016 at 20:37, Andreas Tille wrote: | Hi again, | | I solved this by simply removing the whole configure script in a quilt patch. That sounds crazy so I took a look. BioConductor just had a 3.3 release (matching the R release cycle) and they seemingly simplified it a lot. Compare these two: https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.2/configure.ac https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.3/configure.ac I did not look too closely at the older one but the newer does check for OpenSSL present or not __and then uses this in src/Makevars.in__ so if it were me I consider switching to this. Or rather, I take the 'self-directory' test out in 3.2. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)
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
