Package: src:bowtie
Version: 1.1.2-2
User: [email protected]
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.
