[Debian-med-packaging] Bug#957131: dialign-t: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 11:58:46 BST 2020
Package: src:dialign-t
Version: 1.0.2-12
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10
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-10/g++-10, but succeeds to build with gcc-9/g++-9. 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/gcc10-20200225/dialign-t_1.0.2-12_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html
[...]
| | |
| long int * int *
| %i
museq.c:278:27: warning: implicit declaration of function ‘free_alignment’ [-Wimplicit-function-declaration]
278 | if(! para->FAST_MODE) free_alignment(algn);
| ^~~~~~~~~~~~~~
io.c:535:35: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
535 | while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
| ~~^ ~~~~
| | |
| long int * int *
| %i
io.c:535:39: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
535 | while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
| ~~^ ~~~~
| | |
| long int * int *
| %i
io.c: In function ‘read_scr_matrix’:
io.c:270:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
270 | fscanf( fp, "%i", &is);
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
282 | fscanf(fp, "%s\n", rline);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function ‘read_diag_prob_dist’:
io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static
1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
| ^~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx -c -o alig.o alig.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx -c -o assemble.o assemble.c
alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
| ^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined
13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
| ^~~~~~~~~~~
assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined
37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
| ^~~~~~~~
assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined
25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
| ^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
| ^~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx -c -o prob.o prob.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx -c -o orf.o orf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx -c -o translate.o translate.c
rm -f ./museq
gcc -o ./museq \
./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o \
-pipe -Wall -lm -Wl,-z,relro -Wl,-z,now
/usr/bin/ld: ./parameters.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./io.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./diag.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./alig.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./assemble.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./prob.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./orf.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
/usr/bin/ld: ./translate.o:./source/parameters.h:141: multiple definition of `para'; ./museq.o:./source/parameters.h:141: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:36: museq] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/source'
dh_auto_build: error: cd source && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:12: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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