[Debian-med-packaging] Bug#957659: paml: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 12:08:18 BST 2020
Package: src:paml
Version: 4.9j+dfsg-1
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/paml_4.9j+dfsg-1_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
[...]
| |
| char **
In file included from baseml.c:11:
paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’
150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
| ~~~~~~~~~~~~~~~^~~~~~~~~
In file included from basemlg.c:80:
treesub.c: In function ‘AllPatterns’:
treesub.c:1361:25: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
1361 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL);
| ~~~^~~~~~~
| |
| unsigned char **
In file included from basemlg.c:11:
paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’
153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
| ~~~~~^~~~~~~~
In file included from codeml.c:238:
treesub.c: In function ‘IdenticalSeqs’:
treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types]
1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
| ~~~^~~~~~~
| |
| char **
In file included from codeml.c:17:
paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’
150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
| ~~~~~~~~~~~~~~~^~~~~~~~~
In file included from mcmctree.c:192:
treesub.c: In function ‘IdenticalSeqs’:
treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types]
1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
| ~~~^~~~~~~
| |
| char **
In file included from mcmctree.c:22:
paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’
150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
| ~~~~~~~~~~~~~~~^~~~~~~~~
mcmctree.c: In function ‘DescriptiveStatisticsSimpleMCMCTREE’:
mcmctree.c:3861:54: warning: ‘%.6g’ directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=]
3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]);
| ^~~~
mcmctree.c:3861:36: note: assuming directive output of 12 bytes
3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
mcmctree.c:3861:7: note: ‘sprintf’ output between 17 and 41 bytes into a destination of size 32
3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/ccWyBqVI.o:./src/paml.h:377: multiple definition of `OutTreeOptions'; /tmp/ccgGSMiD.o:./src/paml.h:377: first defined here
/usr/bin/ld: /tmp/ccWyBqVI.o:./src/paml.h:375: multiple definition of `SeqTypes'; /tmp/ccgGSMiD.o:./src/paml.h:375: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:14: basemlg] Error 1
make[1]: *** Waiting for unfinished jobs....
/usr/bin/ld: /tmp/ccB2LMZ0.o:./src/paml.h:377: multiple definition of `OutTreeOptions'; /tmp/ccub7WZN.o:./src/paml.h:377: first defined here
/usr/bin/ld: /tmp/ccB2LMZ0.o:./src/paml.h:375: multiple definition of `SeqTypes'; /tmp/ccub7WZN.o:./src/paml.h:375: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:22: mcmctree] Error 1
/usr/bin/ld: /tmp/cc0wic2e.o:./src/paml.h:377: multiple definition of `OutTreeOptions'; /tmp/ccg1QRDT.o:./src/paml.h:377: first defined here
/usr/bin/ld: /tmp/cc0wic2e.o:./src/paml.h:375: multiple definition of `SeqTypes'; /tmp/ccg1QRDT.o:./src/paml.h:375: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:12: baseml] Error 1
/usr/bin/ld: /tmp/ccnIGTRB.o:./src/paml.h:377: multiple definition of `OutTreeOptions'; /tmp/ccccQug6.o:./src/paml.h:377: first defined here
/usr/bin/ld: /tmp/ccnIGTRB.o:./src/paml.h:375: multiple definition of `SeqTypes'; /tmp/ccccQug6.o:./src/paml.h:375: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:16: codeml] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:13: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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