[Debian-med-packaging] Bug#806220: bowtie: FTBFS when built with dpkg-buildpackage -A (Directory nonexistent)

[Santiago Vila]

Package: src:bowtie
Version: 1.1.2-2
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
   dh_testdir -i
   dh_auto_configure -i
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make allall
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -O3 -DCOMPILER_OPTIONS="\"-O3  -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro\""  -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro  \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
	-I /usr/include/seqan \
	-o bowtie-build-s ebwt_build.cpp \

[... snipped ...]

example3 OK
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments to 1 output stream(s)
example4 OK
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 5 alignments to 1 output stream(s)
example5 OK
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments to 1 output stream(s)
example6 OK
example7 OK
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 5 alignments to 1 output stream(s)
example8 OK
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments to 1 output stream(s)
example9 OK
rm -f tests examples[0-9].out
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 fakeroot debian/rules binary-indep
dh binary-indep
   dh_testroot -i
   dh_prep -i
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
help2man --name="ultrafast memory-efficient short read aligner" --no-info \
             /<<PKGBUILDDIR>>/bowtie > /<<PKGBUILDDIR>>/debian/bowtie/usr/share/man/man1/bowtie.1
/bin/sh: 1: cannot create /<<PKGBUILDDIR>>/debian/bowtie/usr/share/man/man1/bowtie.1: Directory nonexistent
debian/rules:20: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:14: 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.

In this case, I see that you are using "dh", which allow
(independently) optional targets override_dh_foo-arch and
override_dh_foo-indep (for several values of "foo").

Maybe using them this problem could be fixed.

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.