[Debian-med-packaging] Bug#984043: ea-utils: ftbfs with GCC-11
Matthias Klose
doko at debian.org
Wed Mar 3 16:11:49 GMT 2021
Package: src:ea-utils
Version: 1.1.2+dfsg-6
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
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
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