[Debian-med-packaging] Bug#805998: bedtools: FTBFS when built with dpkg-buildpackage -A (No such file or directory)

[Santiago Vila]

Package: src:bedtools
Version: 2.25.0-1
User: sanvila at debian.org
Usertags: binary-indep
Severity: important

Dear maintainer:

I tried to build this package with "dpkg-buildpackage -A"
(i.e. only architecture-independent packages), and it failed:

--------------------------------------------------------------------------------
[...]
 fakeroot debian/rules binary-indep
dh binary-indep
   dh_testroot -i
   dh_prep -i
	rm -f debian/bedtools-test.substvars
	rm -f debian/bedtools-test.*.debhelper
	rm -rf debian/bedtools-test/
   dh_auto_install -i
	install -d debian/bedtools-test
	make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.25.0
CURRENT_VERSION  = v2.25.0
 * Creating BamTools API
- Building in src/utils/bedFile
make[2]: '../../../obj//bedFile.o' is up to date.
- Building in src/utils/BinTree
make[2]: '../../../obj//BinTree.o' is up to date.
- Building in src/utils/version
make[2]: Nothing to be done for 'all'.

[... snipped ...]

	find debian/bedtools-test/usr/include -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/bedtools-test/usr/share/applications -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/bedtools-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/bedtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm'  -print0 2>/dev/null | xargs -0r chmod a-X
	find debian/bedtools-test -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \)  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/bedtools-test/usr/lib -type f -name '*.ali'  -print0 2>/dev/null | xargs -0r chmod uga-w
chmod -x /<<PKGBUILDDIR>>/debian/bedtools/usr/share/bedtools/genomes/*.genome
chmod: cannot access '/<<PKGBUILDDIR>>/debian/bedtools/usr/share/bedtools/genomes/*.genome': No such file or directory
debian/rules:29: recipe for target 'override_dh_fixperms' failed
make[1]: *** [override_dh_fixperms] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:11: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep gave error exit status 2
--------------------------------------------------------------------------------

Sorry not to have a fix, as I am reporting many bugs similar to
this one, but I can give some general hints:

* If all the arch-independent packages are dummy transitional packages
released with jessie, the easy fix is to drop them now.
 
* If not, debian/rules should be modified so that the binary-indep
target works in all cases, even when binary-arch is not used (this is
what the "Architecture: all" autobuilder does). For that:
    
* If you are using debhelper, you might want to use options -a and -i
for dh_* commands so that they do not act on packages they do not
have to act.

* Also, if you are using dh, the (independently) optional targets
override_dh_foo-arch and override_dh_foo-indep (for several values
of "foo") may be useful to write a debian/rules which behaves exactly
as desired.


After checking that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B"
work properly, this package will be suitable to be uploaded in
source-only form if you wish (you might want to try it).

Thanks.