Your message dated Sat, 17 Aug 2019 17:06:25 +0000
with message-id <e1hz29p-000gzo...@fasolo.debian.org>
and subject line Bug#925728: fixed in lagan 2.0-5
has caused the Debian Bug report #925728,
regarding lagan: ftbfs with GCC-9
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 ow...@bugs.debian.org
immediately.)
--
925728: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925728
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:lagan
Version: 2.0-3
Severity: normal
Tags: sid bullseye
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-9
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-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/lagan_2.0-3_unstable_gcc9.log
The last lines of the build log are at the end of this report.
To build with GCC 9, either set CC=gcc-9 CXX=g++-9 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-9/porting_to.html
GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.
[...]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -o ../utils/cextract utils/cextract.c
-Wl,-z,relro
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -o ../utils/cstat utils/cstat.c
-Wl,-z,relro
utils/cstat.c: In function 'cntlets':
utils/cstat.c:51:10: warning: implicit declaration of function 'isspace'
[-Wimplicit-function-declaration]
51 | if (!isspace(currchar)) {
| ^~~~~~~
utils/cstat.c:52:18: warning: implicit declaration of function 'toupper'
[-Wimplicit-function-declaration]
52 | currchar = toupper(currchar);
| ^~~~~~~
filebuffer.c: In function 'FileRead':
filebuffer.c:123:34: warning: implicit declaration of function 'toupper'
[-Wimplicit-function-declaration]
123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
| ^~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -o ../utils/contigorder
utils/contigorder.c -Wl,-z,relro
utils/contigorder.c: In function 'getFileInfo':
utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *'
argument [-Wformat=]
15 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char *
utils/contigorder.c:26:18: warning: unknown conversion type character '&' in
format [-Wformat=]
26 | fscanf (file, "%&d", &dummy);
| ^
utils/contigorder.c:26:16: warning: too many arguments for format
[-Wformat-extra-args]
26 | fscanf (file, "%&d", &dummy);
| ^~~~~
utils/contigorder.c: In function 'getScores':
utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *'
argument [-Wformat=]
52 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char *
/usr/bin/ld: /tmp/ccUM9c0s.o: in function `connectToPrev':
./src/fchaos.c:532: undefined reference to `findPrev'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:14: ../chaos] Error 1
make[2]: *** Waiting for unfinished jobs....
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int',
but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
filebuffer.c: In function 'FileRead':
filebuffer.c:123:34: warning: implicit declaration of function 'toupper'
[-Wimplicit-function-declaration]
123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
| ^~~~~~~
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int',
but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
filebuffer.c: In function 'FileRead':
filebuffer.c:123:34: warning: implicit declaration of function 'toupper'
[-Wimplicit-function-declaration]
123 | temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
| ^~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: cd src && make -j4 "INSTALL=install --strip-program=true"
returned exit code 2
make[1]: *** [debian/rules:9: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit
status 2
--- End Message ---
--- Begin Message ---
Source: lagan
Source-Version: 2.0-5
We believe that the bug you reported is fixed in the latest version of
lagan, 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 925...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Steffen Moeller <moel...@debian.org> (supplier of updated lagan 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 16 Aug 2019 19:49:41 +0200
Source: lagan
Binary: lagan lagan-dbgsym
Architecture: source amd64
Version: 2.0-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Steffen Moeller <moel...@debian.org>
Description:
lagan - highly parametrizable pairwise global genome sequence aligner
Closes: 925728
Changes:
lagan (2.0-5) unstable; urgency=medium
.
* Team upload
.
[ Gianfranco Costamagna ]
* removed "inline" helps to avoid FTBFS (Closes: #925728)
.
[ Steffen Moeller ]
* <ctype.h> included to help FTBFS
* verbose builds, please
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