Bug#957194: marked as done (fastlink: ftbfs with GCC-10)

[Debian Bug Tracking System]

Your message dated Fri, 30 Oct 2020 09:18:29 +0000
with message-id <e1kyqyh-0000kk...@fasolo.debian.org>
and subject line Bug#957194: fixed in fastlink 4.1P-fix100+dfsg-3
has caused the Debian Bug report #957194,
regarding fastlink: ftbfs with GCC-10
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.)


-- 
957194: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957194
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:fastlink
Version: 4.1P-fix100+dfsg-2
Severity: normal
Tags: sid bullseye
User: debian-...@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/fastlink_4.1P-fix100+dfsg-2_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

[...]
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:864: multiple definition of 
`continue_'; loiostuff.o:./4.1P/src/commondefs.h:864: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:674: multiple definition of 
`maxmemcount'; loiostuff.o:./4.1P/src/commondefs.h:674: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:674: multiple definition of 
`memcount'; loiostuff.o:./4.1P/src/commondefs.h:674: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:671: multiple definition of 
`ped_nuscales'; loiostuff.o:./4.1P/src/commondefs.h:671: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:640: multiple definition of 
`looplastgen'; loiostuff.o:./4.1P/src/commondefs.h:640: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:637: multiple definition of 
`loopfirstgen'; loiostuff.o:./4.1P/src/commondefs.h:637: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:626: multiple definition of 
`loopfile'; loiostuff.o:./4.1P/src/commondefs.h:626: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:624: multiple definition of 
`speedfile'; loiostuff.o:./4.1P/src/commondefs.h:624: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:624: multiple definition of 
`ipedfile'; loiostuff.o:./4.1P/src/commondefs.h:624: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:622: multiple definition of 
`disfreqs'; loiostuff.o:./4.1P/src/commondefs.h:622: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:619: multiple definition of 
`risk'; loiostuff.o:./4.1P/src/commondefs.h:619: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:618: multiple definition of 
`segscale'; loiostuff.o:./4.1P/src/commondefs.h:618: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:614: multiple definition of 
`lastpriv'; loiostuff.o:./4.1P/src/commondefs.h:614: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:614: multiple definition of 
`risksys'; loiostuff.o:./4.1P/src/commondefs.h:614: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:612: multiple definition of 
`riskall'; loiostuff.o:./4.1P/src/commondefs.h:612: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:608: multiple definition of 
`segval'; loiostuff.o:./4.1P/src/commondefs.h:608: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:607: multiple definition of 
`tempseg2'; loiostuff.o:./4.1P/src/commondefs.h:607: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:607: multiple definition of 
`tempseg'; loiostuff.o:./4.1P/src/commondefs.h:607: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:606: multiple definition of 
`segindex'; loiostuff.o:./4.1P/src/commondefs.h:606: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:604: multiple definition of 
`genenumber'; loiostuff.o:./4.1P/src/commondefs.h:604: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:603: multiple definition of 
`muthap'; loiostuff.o:./4.1P/src/commondefs.h:603: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:600: multiple definition of 
`numCopies'; loiostuff.o:./4.1P/src/commondefs.h:600: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:599: multiple definition of 
`looppers'; loiostuff.o:./4.1P/src/commondefs.h:599: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:594: multiple definition of 
`phapcache1'; loiostuff.o:./4.1P/src/commondefs.h:594: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:586: multiple definition of 
`qsumcache'; loiostuff.o:./4.1P/src/commondefs.h:586: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:586: multiple definition of 
`psumcache'; loiostuff.o:./4.1P/src/commondefs.h:586: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:581: multiple definition of 
`gene'; loiostuff.o:./4.1P/src/commondefs.h:581: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:580: multiple definition of 
`flag'; loiostuff.o:./4.1P/src/commondefs.h:580: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:578: multiple definition of 
`nonzgens'; loiostuff.o:./4.1P/src/commondefs.h:578: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:577: multiple definition of 
`order'; loiostuff.o:./4.1P/src/commondefs.h:577: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:574: multiple definition of 
`probend'; loiostuff.o:./4.1P/src/commondefs.h:574: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:574: multiple definition of 
`probstart'; loiostuff.o:./4.1P/src/commondefs.h:574: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:573: multiple definition of 
`segstart'; loiostuff.o:./4.1P/src/commondefs.h:573: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:572: multiple definition of 
`nchild'; loiostuff.o:./4.1P/src/commondefs.h:572: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:571: multiple definition of 
`childarray'; loiostuff.o:./4.1P/src/commondefs.h:571: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:569: multiple definition of 
`thischild'; loiostuff.o:./4.1P/src/commondefs.h:569: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:567: multiple definition of 
`malechild'; loiostuff.o:./4.1P/src/commondefs.h:567: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:564: multiple definition of 
`riskmale'; loiostuff.o:./4.1P/src/commondefs.h:564: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of 
`risk2'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of 
`risk1'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of 
`rare'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:561: multiple definition of 
`thispath'; loiostuff.o:./4.1P/src/commondefs.h:561: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:554: multiple definition of 
`invgenenum2'; loiostuff.o:./4.1P/src/commondefs.h:554: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:554: multiple definition of 
`invgenenum1'; loiostuff.o:./4.1P/src/commondefs.h:554: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:550: multiple definition of 
`hind'; loiostuff.o:./4.1P/src/commondefs.h:550: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:549: multiple definition of 
`haps2'; loiostuff.o:./4.1P/src/commondefs.h:549: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:549: multiple definition of 
`haps1'; loiostuff.o:./4.1P/src/commondefs.h:549: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:548: multiple definition of 
`fence'; loiostuff.o:./4.1P/src/commondefs.h:548: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:548: multiple definition of 
`base'; loiostuff.o:./4.1P/src/commondefs.h:548: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:547: multiple definition of 
`currentfence'; loiostuff.o:./4.1P/src/commondefs.h:547: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:536: multiple definition of 
`maxfemgen'; loiostuff.o:./4.1P/src/commondefs.h:536: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:536: multiple definition of 
`maxhaplo'; loiostuff.o:./4.1P/src/commondefs.h:536: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:532: multiple definition of 
`mymaxped'; loiostuff.o:./4.1P/src/commondefs.h:532: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:531: multiple definition of 
`pedidx2num'; loiostuff.o:./4.1P/src/commondefs.h:531: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:530: multiple definition of 
`currentped'; loiostuff.o:./4.1P/src/commondefs.h:530: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:529: multiple definition of 
`ped_loc_all'; loiostuff.o:./4.1P/src/commondefs.h:529: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:518: multiple definition of 
`ped_must_change_locations'; loiostuff.o:./4.1P/src/commondefs.h:518: first 
defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:513: multiple definition of 
`ped_new_allele_count'; loiostuff.o:./4.1P/src/commondefs.h:513: first defined 
here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:493: multiple definition of 
`gfemaletheta'; loiostuff.o:./4.1P/src/commondefs.h:493: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:493: multiple definition of 
`gmaletheta'; loiostuff.o:./4.1P/src/commondefs.h:493: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:356: multiple definition of 
`approxarray'; loiostuff.o:./4.1P/src/commondefs.h:356: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:661: lodscore] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/4.1P/src'
dh_auto_build: error: cd 4.1P/src && make -j4 "INSTALL=install 
--strip-program=true" "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. 
-fstack-protector-strong -Wformat -Werror=format-security" 
"DEBIANLDFLAGS=-Wl,-z,relro -Wl,-z,now" returned exit code 2
make[1]: *** [debian/rules:12: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

--- End Message ---

--- Begin Message ---

Source: fastlink
Source-Version: 4.1P-fix100+dfsg-3
Done: Andreas Tille <ti...@debian.org>

We believe that the bug you reported is fixed in the latest version of
fastlink, 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 957...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated fastlink 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, 30 Oct 2020 10:02:10 +0100
Source: fastlink
Architecture: source
Version: 4.1P-fix100+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 957194
Changes:
 fastlink (4.1P-fix100+dfsg-3) unstable; urgency=medium
 .
   * Add fake watch file
   * debian/get-orig-source: Do not create new tarball if there is no new
     patchlevel
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 13 (routine-update)
   * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
     update)
   * Remove trailing whitespace in debian/changelog (routine-update)
   * Add salsa-ci file (routine-update)
   * Rules-Requires-Root: no (routine-update)
   * Refer to specific version of license GPL-2+.
   * Use -fcommon option to tolerate "multiple definition of"
     Closes: #957194
   * Propagate CFLAGS set by Debian to all binaries
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fastlink_4.1P-fix100+dfsg-3.debian.tar.xz
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fastlink_4.1P-fix100+dfsg-3_amd64.buildinfo
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Files:
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fastlink_4.1P-fix100+dfsg-3.dsc
 0d5e7a59d39bcceaac15d3a56df0727d 22384 science optional 
fastlink_4.1P-fix100+dfsg-3.debian.tar.xz
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fastlink_4.1P-fix100+dfsg-3_amd64.buildinfo

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--- End Message ---