[pkg-bioc] Problem building CRAN packages

[Dirk Eddelbuettel]

Hi Johannes,

And a CC to Andrew who may be joining the fun shortly...

On 20 June 2006 at 10:27, Johannes Ranke wrote:
| Dear all,
| 
| After fixing a small typo in cran2deb.pl (committed), and adding a
| couple of build-dependencies to the 
| 
| 	  ## List of packages that build once their dependencies are
| 	  ## available in the build environment.
| 
| (not committed), I have successfully built 485 packages so far.

Pretty good start!  Congrats! 

I only got 461 when I played with some modifications a few weeks ago.... Some
of my changed are still not checked in, and I am not sure if it makes sense
now. 

| Meanwhile, I would like to address three issues:
| 
| 1) Why are these dependencies not handled in the array that seems to
| be made for build dependencies:
| 
| 	my %buildDeps=(
| 	           arules    => ["r-cran-matrix"], ##
| 				...
| 				...

Not sure I understand the question.  Are you asking why particular
dependencies are missing?  That could be simply because the script has not
been updated in a while.
 
| 2) At the moment, I repeatedly encounter failures like
| 
| building package builds/r-cran-pcurve_0.6.2-0.r2d.1_amd64.deb ...
| debuild: fatal error at line 1224:
| fakeroot debian/rules binary failed
| fakeroot debian/rules clean
| dpkg-source -b pcurve-0.6.2
| dpkg-source: cannot represent change to src/Getlam.o: binary file
| contents changed
| dpkg-source: warning: executable mode 0755 of `src/pcurve.so' will not
| be represented in diff
| dpkg-source: cannot represent change to src/pcurve.so: binary file
| contents changed
| dpkg-source: unrepresentable changes to source

Standard building errors indicating that the directory wasn't cleaned which
should happen from 'R CMD INSTALL' as well as from the script which removes
directories.   There must be a reason that failed here..

| dpkg-buildpackage: source package is pcurve
| dpkg-buildpackage: source version is 0.6.2-0.r2d.1
| dpkg-buildpackage: source changed by CRAN/BioC packagers
| <pkg-bioc-devel at lists.alioth.debian.org>
| dpkg-buildpackage: host architecture amd64
| dpkg-buildpackage: source version without epoch 0.6.2-0.r2d.1
| test -x debian/rules
| test "`id -u`" = 0
| dh_clean
| dpkg-source: building pcurve using existing pcurve_0.6.2.orig.tar.gz
| dpkg-source: building pcurve in pcurve_0.6.2-0.r2d.1.diff.gz
| dpkg-source: building pcurve in pcurve_0.6.2-0.r2d.1.dsc
| build failed for builds/r-cran-pcurve_0.6.2-0.r2d.1_amd64.deb built in
| builds/pcurve-0.6.2
| 
| What is the problem? The format of the source version string?

No, I think the build errors above drive that...

| 3) Did anybody ever create a condensed version of cran2deb.pl for
| building just an exactly defined subset of packages? I'd be interested.

We need to redo the script, at least in parts. The "big loop" around the core
is hundreds of lines.

If and when it has been refactored, it should be possible to call for just
one file.  In fact we could even rearchitecture such that each call is
treated like just one (re-reading the meta information may be costly that
way, though).

Hope this helps, Dirk

| Best regards,
| 
| Johannes
| 
| -- 
| Dr. Johannes Ranke                 jranke at uni-bremen.de
| UFT Bremen, Leobenerstr. 1         +49 421 218 8971 
| D-28359 Bremen                     http://www.uft.uni-bremen.de/chemie/ranke
| 

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison