[Debian-med-packaging] Bug#806223: theseus: FTBFS when built with dpkg-buildpackage -A (Directory nonexistent)

[Santiago Vila]

Package: src:theseus
Version: 3.3.0-3
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
   dh_auto_build -i
	make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
( cd libdistfit; make && cp libdistfit.a ../lib  )
make[2]: Entering directory '/<<PKGBUILDDIR>>/libdistfit'
/usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result -pthread  -c statistics.c
/usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result -pthread  -c beta_dist.c
/usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result -pthread  -c betaprime_dist.c

[... snipped ...]

a - MultiPose.o
a - MultiPose2MSA.o
a - MultiPosePth.o
a - PCAstats.o
a - pdbIO.o
a - pdbMalloc.o
a - pdbStats.o
a - pdbUtils.o
a - QuarticHornFrag.o
a - RandCds.o
a - pdbSSM.o
a - ProcGSLSVD.o
a - ProcGSLSVDNu.o
a - ProcJacobiSVD.o
a - GibbsMet.o
a - qcprot.o
a - StructAlign.o
a - NWfill.o
a - termcol.o
a - theseuslib.o
mv libtheseus.a lib/libtheseus.a
ranlib lib/libtheseus.a
/usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result -pthread  -c theseus.c
/usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result -pthread -Wl,-z,relro -L./lib theseus.o CovMat.o DistMat.o Embed.o  Error.o FragCds.o FragDist.o HierarchVars.o lodmats.o MultiPose.o MultiPose2MSA.o MultiPosePth.o PCAstats.o pdbIO.o pdbMalloc.o pdbStats.o pdbUtils.o QuarticHornFrag.o RandCds.o pdbSSM.o ProcGSLSVD.o ProcGSLSVDNu.o ProcJacobiSVD.o GibbsMet.o qcprot.o StructAlign.o NWfill.o termcol.o theseuslib.o -lgsl -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus -lpthread -lgsl -lgslcblas -lm -lc -o theseus
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -i
 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>>'
# Fix wrong path used in upstream script.  Fixing it here is safer than
# changing the patch for any new upstream release
sed -e 's?/usr/local/bin?/usr/bin?' \
    -e 's?/usr/bin/sed?/bin/sed?'   \
    theseus_align > debian/theseus/usr/bin/theseus_align
/bin/sh: 1: cannot create debian/theseus/usr/bin/theseus_align: Directory nonexistent
debian/rules:12: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:9: 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.