Your message dated Sun, 17 Oct 2021 20:21:24 +0000
with message-id <[email protected]>
and subject line Bug#984043: fixed in ea-utils 1.1.2+dfsg-9
has caused the Debian Bug report #984043,
regarding ea-utils: ftbfs with GCC-11
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.)
--
984043: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984043
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ea-utils
Version: 1.1.2+dfsg-6
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye release]
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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/ea-utils_1.1.2+dfsg-6_unstable_gcc11.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security fastq-lib.cpp -o fastq-clipper fastq-clipper.c
-Wl,-z,relro -Wl,-z,now
fastq-lib.cpp: In function ‘int getstr(char**, size_t*, FILE*, char, int)’:
fastq-lib.cpp:284:20: warning: ISO C++17 does not allow ‘register’ storage
class specifier [-Wregister]
284 | register int c = getc (stream);
| ^
fastq-mcf.c: In function ‘int main(int, char**)’:
fastq-mcf.c:633:65: warning: too many arguments for format [-Wformat-extra-args]
633 | fprintf(stderr,
"Warning, corrupt quality for sequence: %s", s, q);
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastq-mcf.c:849:56: warning: too many arguments for format [-Wformat-extra-args]
849 | fprintf(fstat, ", warning end
was not reliable\n", ad[a].id, ad[a].seq);
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastq-mcf.c: In function ‘bool arg_int_pair(const char*, int&, int&)’:
fastq-mcf.c:1657:6: warning: control reaches end of non-void function
[-Wreturn-type]
1657 | b=atoi(strchr(optarg, ',')+1);
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security fastq-lib.cpp sam-stats.cpp -lbam -lz
-lpthread -o sam-stats -Wl,-z,relro -Wl,-z,now
fastq-lib.cpp: In function ‘int getstr(char**, size_t*, FILE*, char, int)’:
fastq-lib.cpp:284:20: warning: ISO C++17 does not allow ‘register’ storage
class specifier [-Wregister]
284 | register int c = getc (stream);
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security fastq-lib.cpp tidx/tidx-lib.cpp -o varcall
varcall.cpp -lgsl -lgslcblas -Wl,-z,relro -Wl,-z,now
fastq-stats.cpp: In function ‘int main(int, char**)’:
fastq-stats.cpp:183:37: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
183 | case 'D': ++nodup; break;
| ^~~~~
fastq-stats.cpp:184:37: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
184 | case 'd': ++debug; break;
| ^~~~~
fastq-stats.cpp:187:61: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
187 | case 'x': fastx_outfile = optarg; ++fastx;
break;
| ^~~~~
fastq-stats.cpp:188:63: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
188 | case 'b': brkdown_outfile = optarg; ++brkdown;
break;
| ^~~~~~~
fastq-stats.cpp:189:37: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
189 | case 'L': ++len_hist; lenhist_outfile = optarg;
break;
| ^~~~~~~~
fastq-stats.cpp:190:58: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
190 | case 'g': gc_outfile = optarg; ++gc; break;
| ^~
fastq-lib.cpp: In function ‘int getstr(char**, size_t*, FILE*, char, int)’:
fastq-lib.cpp:284:20: warning: ISO C++17 does not allow ‘register’ storage
class specifier [-Wregister]
284 | register int c = getc (stream);
| ^
make[1]: *** [Makefile:94: fastq-stats] Error 1
make[1]: *** Waiting for unfinished jobs....
sam-stats.cpp: In function ‘int main(int, char**)’:
sam-stats.cpp:229:29: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
229 | case 'D': ++trackdup; break;
| ^~~~~~~~
sam-stats.cpp: In member function ‘int ibucket::operator[](int) const’:
sam-stats.cpp:140:9: warning: control reaches end of non-void function
[-Wreturn-type]
140 | }
| ^
make[1]: *** [Makefile:81: sam-stats] Error 1
varcall.cpp: In member function ‘vfinal& vfinal::operator=(const vfinal&)’:
varcall.cpp:128:122: warning: no return statement in function returning
non-void [-Wreturn-type]
128 | vfinal & operator=(vfinal const&x) {max_idl_seq=x.max_idl_seq;
max_idl_cnt=x.max_idl_cnt; padj=x.padj; pcall=x.pcall;}
|
^
|
return *this;
varcall.cpp: In member function ‘virtual void
VarStatVisitor::Visit(PileupSummary&)’:
varcall.cpp:1584:33: warning: too many arguments for format
[-Wformat-extra-args]
1584 | fprintf(noise_f,"%d\t%c\t%f\t%f\n", p.Depth, pbase,
noise, qnoise, mnqual);
| ^~~~~~~~~~~~~~~~~~
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:13: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: ea-utils
Source-Version: 1.1.2+dfsg-9
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ea-utils, 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.
Étienne Mollier <[email protected]> (supplier of updated ea-utils 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: SHA512
Format: 1.8
Date: Sun, 17 Oct 2021 21:37:07 +0200
Source: ea-utils
Architecture: source
Version: 1.1.2+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 984043
Changes:
ea-utils (1.1.2+dfsg-9) unstable; urgency=medium
.
* Team upload.
* Add gcc11.patch to fix ftbfs with gcc 11. (Closes: #984043)
Checksums-Sha1:
ecece84ef6bdeea16148d33ee0dfb495449b0177 2098 ea-utils_1.1.2+dfsg-9.dsc
e2589d9bb18a6c20735ebecfa112a2b672728955 32412
ea-utils_1.1.2+dfsg-9.debian.tar.xz
294bbe0fa1b337bc95069ee983dd334b16aa9dfd 6047
ea-utils_1.1.2+dfsg-9_amd64.buildinfo
Checksums-Sha256:
89887032ae57f3b82f5034e86d087730f9a772de2e2924a580b7686414d46d48 2098
ea-utils_1.1.2+dfsg-9.dsc
a3900019c7f63cb3d585438d920948123504ba9a0f2a8197a062848a7adf8213 32412
ea-utils_1.1.2+dfsg-9.debian.tar.xz
77c8b8eb62d44fabb5fbc956aec459157524afa87236ab2cc2b8a2b52051bdfb 6047
ea-utils_1.1.2+dfsg-9_amd64.buildinfo
Files:
9a6004d62f98f7eef2066ff0b06a94e4 2098 science optional
ea-utils_1.1.2+dfsg-9.dsc
a2615385ce5fee70026db58441c2c8e0 32412 science optional
ea-utils_1.1.2+dfsg-9.debian.tar.xz
59c5e0635b5224397da5fa273ec3119f 6047 science optional
ea-utils_1.1.2+dfsg-9_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=tJda
-----END PGP SIGNATURE-----
--- End Message ---
