Your message dated Wed, 25 Nov 2015 17:19:21 +0000
with message-id <[email protected]>
and subject line Bug#806223: fixed in theseus 3.3.0-4
has caused the Debian Bug report #806223,
regarding theseus: 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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
806223: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806223
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:theseus
Version: 3.3.0-3
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
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.
--- End Message ---
--- Begin Message ---
Source: theseus
Source-Version: 3.3.0-4
We believe that the bug you reported is fixed in the latest version of
theseus, 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 theseus 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 18:01:44 +0100
Source: theseus
Binary: theseus theseus-examples
Architecture: source all amd64
Version: 3.3.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
theseus - superimpose macromolecules using maximum likelihood
theseus-examples - superimpose macromolecules using maximum likelihood
(examples)
Closes: 806223
Changes:
theseus (3.3.0-4) unstable; urgency=medium
.
* Enable building arch independent packages separately
Closes: #806223
* Build against libgsl-dev (version 2) rather than libgsl0-dev
* Add autopkgtest
Checksums-Sha1:
f6e287855314d5f3d862914262f0dd84c41c2010 2071 theseus_3.3.0-4.dsc
247bab955fb3a757c0eee15ff6f91f3b62e92ed7 10300 theseus_3.3.0-4.debian.tar.xz
7166ecde2c9eb94ae7cc6123a07d5c3d150a810f 20836598
theseus-examples_3.3.0-4_all.deb
ea47c5d226cad4b3736b4da8128df9cc5367cb29 421154 theseus_3.3.0-4_amd64.deb
Checksums-Sha256:
b214895d6d18195934f8b90556fb12cbe5df6798da2f6cea4347cbefc25e014d 2071
theseus_3.3.0-4.dsc
d5e6557eeb41e67af7c5a01ae00318e3c07ecb1b3b5b6e7b374ece108594cda9 10300
theseus_3.3.0-4.debian.tar.xz
c6e9e76025d1ded2f3a72d8f0b021aa2412cd7c119766f32729c8f0c9a4c7fce 20836598
theseus-examples_3.3.0-4_all.deb
19fe0f0de72bb88a8e6807fc1d27a88bf719aaa0354cfc9cd28a3e45b32925e9 421154
theseus_3.3.0-4_amd64.deb
Files:
2eee15e93b938e4631dbd33970a1dd32 2071 science optional theseus_3.3.0-4.dsc
e8f90fd1eb1e78ecaa6f6d1c27cf51ef 10300 science optional
theseus_3.3.0-4.debian.tar.xz
97d7306a99726e84fda9e973cb94e787 20836598 science optional
theseus-examples_3.3.0-4_all.deb
de54896f1c88bcd3de20c91a02b9adee 421154 science optional
theseus_3.3.0-4_amd64.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1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=G+6+
-----END PGP SIGNATURE-----
--- End Message ---
