Your message dated Fri, 14 Dec 2018 09:36:14 +0000
with message-id <[email protected]>
and subject line Bug#897877: fixed in trinityrnaseq 2.6.6+dfsg-1
has caused the Debian Bug report #897877,
regarding trinityrnaseq: ftbfs with GCC-8
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.)
--
897877: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897877
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:trinityrnaseq
Version: 2.5.1+dfsg-2
Severity: normal
Tags: sid buster
User: [email protected]
Usertags: ftbfs-gcc-8
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.
The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/trinityrnaseq_2.5.1+dfsg-2_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 8, either set CC=gcc-8 CXX=g++-8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-8/porting_to.html
[...]
mv slclust ../bin/
make[3]: Leaving directory
'/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg/trinity-plugins/slclust/src'
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
dh_install -a
dh_install: Cannot find (any matches for) "Chrysalis/TranscriptomeFromVaryK"
(tried in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/TranscriptomeFromVaryK
dh_install: Cannot find (any matches for) "Chrysalis/RunButterfly" (tried in .,
debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/RunButterfly
dh_install: Cannot find (any matches for)
"Chrysalis/ReadsToTranscripts_MPI_chang" (tried in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI_chang
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI"
(tried in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts" (tried
in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts
dh_install: Cannot find (any matches for) "Chrysalis/QuantifyGraph" (tried in
., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/QuantifyGraph
dh_install: Cannot find (any matches for) "Chrysalis/JoinTransByPairs" (tried
in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/JoinTransByPairs
dh_install: Cannot find (any matches for) "Chrysalis/IsoformAugment" (tried in
., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/IsoformAugment
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta_MPI" (tried
in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta_MPI
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta" (tried in
., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta
dh_install: Cannot find (any matches for) "Chrysalis/CreateIwormFastaBundle"
(tried in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/CreateIwormFastaBundle
dh_install: Cannot find (any matches for) "Chrysalis/Chrysalis" (tried in .,
debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/Chrysalis
dh_install: Cannot find (any matches for) "Chrysalis/BreakTransByPairs" (tried
in ., debian/tmp)
dh_install: trinityrnaseq missing files: Chrysalis/BreakTransByPairs
dh_install: missing files, aborting
make[1]: *** [debian/rules:46: override_dh_install-arch] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
make: *** [debian/rules:19: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned
exit status 2
--- End Message ---
--- Begin Message ---
Source: trinityrnaseq
Source-Version: 2.6.6+dfsg-1
We believe that the bug you reported is fixed in the latest version of
trinityrnaseq, 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 trinityrnaseq 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: Fri, 14 Dec 2018 08:58:49 +0100
Source: trinityrnaseq
Binary: trinityrnaseq trinityrnaseq-examples
Architecture: source
Version: 2.6.6+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
trinityrnaseq - RNA-Seq De novo Assembly
trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing
files
Closes: 897877
Changes:
trinityrnaseq (2.6.6+dfsg-1) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* New upstream release, now with the sample data returned
Closes: #897877
* Build and ship seqtk-trinity
.
[ Andreas Tille ]
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Secure URI in copyright format
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
* Fix permissions and Perl interpreter path
Checksums-Sha1:
283cf7584721e2e9e36a8226fddb32183048cb5f 2303 trinityrnaseq_2.6.6+dfsg-1.dsc
00bd94c87036c3c0eaa84bd294b0f0c0b4c5324a 233147280
trinityrnaseq_2.6.6+dfsg.orig.tar.xz
1fe12ab72cdd404431c49abd283cce6bf678fe65 21216
trinityrnaseq_2.6.6+dfsg-1.debian.tar.xz
Checksums-Sha256:
e442b6a2f7b13020ab5ad54380f087d45dfb43b34dcdda6fed47a5ad0954d100 2303
trinityrnaseq_2.6.6+dfsg-1.dsc
2e551b2acdc530d542b0b717b6bb6e124ac49416e68da65e213fb104486c4a34 233147280
trinityrnaseq_2.6.6+dfsg.orig.tar.xz
30f7adb7a55591a71912436dd222274f9a4bb630acc0a21e882eaa6ca07a7056 21216
trinityrnaseq_2.6.6+dfsg-1.debian.tar.xz
Files:
9a98761e946da8b42d5e2a66af1f8c71 2303 science optional
trinityrnaseq_2.6.6+dfsg-1.dsc
fcd4c7f246b355da4284d7104e74dd54 233147280 science optional
trinityrnaseq_2.6.6+dfsg.orig.tar.xz
66b1af4adefdf6b1c1915bd7b307ad2f 21216 science optional
trinityrnaseq_2.6.6+dfsg-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=l5Ug
-----END PGP SIGNATURE-----
--- End Message ---
