[Debian-med-packaging] Bug#806618: gbrowse: FTBFS when built with dpkg-buildpackage -A (mv: target is not a directory)

[Santiago Vila]

Package: src:gbrowse
Version: 2.54+dfsg-5
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:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with apache2
   dh_testdir -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/gbrowse-2.54+dfsg'
dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
	perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2" --config "ld=cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
Possible precedence issue with control flow operator at /<<BUILDDIR>>/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 1032.
Checking prerequisites...
  recommends:
    *  Bio::DB::BigFile is not installed
    *  Bio::DB::Sam is not installed

[... snipped ...]

Performing variable substitutions in blib/conf/yeast_simple.conf
Performing variable substitutions in blib/htdocs/annotation_help.html
Performing variable substitutions in blib/htdocs/cloud_index.html
Performing variable substitutions in blib/htdocs/example_scripts/index.html
Performing variable substitutions in blib/htdocs/example_scripts/README
Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
Performing variable substitutions in blib/htdocs/general_help.html
Performing variable substitutions in blib/htdocs/index.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf
Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html
Performing variable substitutions in blib/htdocs/vbox_index.html
Performing variable substitutions in blib/etc/default/gbrowse-slave
Performing variable substitutions in blib/etc/init.d/gbrowse-slave
Use of uninitialized value $wwwuser in substitution (s///) at /<<BUILDDIR>>/gbrowse-2.54+dfsg/install_util/GBrowseInstall.pm line 821, <GEN89> line 20.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing debian/gbrowse/etc/init.d/gbrowse-slave
Installing debian/gbrowse/etc/default/gbrowse-slave
Installing debian/gbrowse/lib/perl5/x86_64-linux-gnu-thread-multi/GBrowse/ConfigData.pm
mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
# Remove arch dependant data
mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/
mv: target 'debian/gbrowse-calign/usr/lib/x86_64-linux-gnu/perl5/5.20/auto/Bio/Graphics/Browser2/CAlign/' is not a directory
debian/rules:18: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/gbrowse-2.54+dfsg'
debian/rules:7: 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. The common hints are:

* If the only architecture-independent packages are dummy transitional
ones and they were released with jessie, the easy fix is to drop them
now.

* When using "dh", it is allowed to use (independently)
optional targets override_dh_foo-arch and override_dh_foo-indep
(for several values of "foo").


Once that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B" work
properly, the package would be suitable to be uploaded in source-only
form if you wish.

Thanks.