Your message dated Wed, 25 Nov 2015 22:19:29 +0000
with message-id <[email protected]>
and subject line Bug#806220: fixed in bowtie 1.1.2-3
has caused the Debian Bug report #806220,
regarding bowtie: FTBFS when built with dpkg-buildpackage -A (Directory
nonexistent)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
806220: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806220
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: bowtie
Source-Version: 1.1.2-3
We believe that the bug you reported is fixed in the latest version of
bowtie, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated bowtie package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 25 Nov 2015 22:38:02 +0100
Source: bowtie
Binary: bowtie bowtie-examples
Architecture: source all amd64
Version: 1.1.2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
bowtie - Ultrafast memory-efficient short read aligner
bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short
read al
Closes: 806220
Changes:
bowtie (1.1.2-3) unstable; urgency=medium
.
* Enable building arch independent packages separately
Closes: #806220
* Fix clean target
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Files:
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--- End Message ---
