Your message dated Mon, 21 Aug 2017 09:04:13 +0000
with message-id <[email protected]>
and subject line Bug#853609: fixed in perm 0.4.0-3
has caused the Debian Bug report #853609,
regarding perm: ftbfs with GCC-7
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
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--
853609: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853609
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:perm
Version: 0.4.0-2
Severity: normal
Tags: sid buster
User: [email protected]
Usertags: ftbfs-gcc-7
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-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/perm_0.4.0-2_unstable_gcc7.log
The last lines of the build log are at the end of this report.
To build with GCC 7, either set CC=gcc-7 CXX=g++-7 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-7/porting_to.html
[...]
MappingResult.h: In function 'bool printAPairedMappingInPerM(FileOutputBuffer*,
CMappingResult&, CMappingResult&, int, bool)':
MappingResult.h:265:26: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:265:48: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:275:26: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:275:48: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
ParameterList.cpp: In member function 'void MappingOpts::setDefaults()':
ParameterList.cpp:31:9: warning: unused variable 'mismatchScoreThreshold'
[-Wunused-variable]
int mismatchScoreThreshold = -1; // No filtering by sum of mismatch score
^~~~~~~~~~~~~~~~~~~~~~
Genome_Index_TableQ.cpp: In member function 'unsigned int
CGenome_Index_TableQ::extendAlignment(CAlignmentsQ&, CReadInBits) const':
Genome_Index_TableQ.cpp:364:10: warning: variable 'extendForward' set but not
used [-Wunused-but-set-variable]
bool extendForward = true;
^~~~~~~~~~~~~
In file included from ReadsQualScores.h:3:0,
from ReadsFileParser.h:19,
from ReadsFileParser.cpp:1:
In function 'char* myStrCpy(char*, const char*, int)',
inlined from 'int CReadsFileParser::initialization()' at
ReadsFileParser.cpp:28:13:
stdafx.h:184:28: warning: 'char* strncpy(char*, const char*, size_t)' writing
4095 bytes into a region of size 2048 overflows the destination
[-Wstringop-overflow=]
char* returnV = strncpy(caBuf, str, iBufSizeMinus1);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from MappingResult.cpp:1:0:
MappingResult.h: In function 'bool printAPairedMappingInPerM(FileOutputBuffer*,
CMappingResult&, CMappingResult&, int, bool)':
MappingResult.h:265:26: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:265:48: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:275:26: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
MappingResult.h:275:48: error: ISO C++ forbids comparison between pointer and
integer [-fpermissive]
if(m1.QScores == '\0' || m2.QScores == '\0') {
^~~~
makefile:26: recipe for target 'perm' failed
make[1]: *** [perm] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j64 returned exit code 2
debian/rules:10: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: perm
Source-Version: 0.4.0-3
We believe that the bug you reported is fixed in the latest version of
perm, 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 perm 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: Mon, 21 Aug 2017 10:07:02 +0200
Source: perm
Binary: perm
Architecture: source amd64
Version: 0.4.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
perm - efficient mapping of short reads with periodic spaced seeds
Closes: 853609
Changes:
perm (0.4.0-3) unstable; urgency=medium
.
* Fix gcc7 issue
Closes: #853609
* Standards-Version: 4.0.1 (no changes needed)
* Remove inactive Uploaders
Checksums-Sha1:
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Files:
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