Bug#957851: marked as done (sweed: ftbfs with GCC-10)

Debian Bug Tracking System Wed, 22 Jul 2020 12:54:35 -0700

Your message dated Wed, 22 Jul 2020 19:50:45 +0000
with message-id <e1jyklj-0006ce...@fasolo.debian.org>
and subject line Bug#957851: fixed in sweed 3.2.1+dfsg-2
has caused the Debian Bug report #957851,
regarding sweed: 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.)


-- 
957851: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957851
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:sweed
Version: 3.2.1+dfsg-1
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/sweed_3.2.1+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

[...]
/usr/bin/ld: SweeD_Input.o:./SweeD.h:140: multiple definition of `nofTokens'; 
SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:138: multiple definition of `map'; 
SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:136: multiple definition of `mainTime0'; 
SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:121: multiple definition of `borderTol'; 
SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:119: multiple definition of 
`linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:117: multiple definition of 
`bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:225: multiple definition of `alignment'; 
SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:257: multiple definition of `clr'; 
SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:245: multiple definition of `factLUT'; 
SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:235: multiple definition of `div6'; 
SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:229: multiple definition of `rvLUT2'; 
SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:228: multiple definition of `rvLUT'; 
SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:227: multiple definition of `rv'; 
SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:142: multiple definition of `nofSamples'; 
SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:140: multiple definition of `nofTokens'; 
SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:138: multiple definition of `map'; 
SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:136: multiple definition of `mainTime0'; 
SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:128: multiple definition of `runName'; 
SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:126: multiple definition of 
`nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:125: multiple definition of 
`VCF_first_SNP'; SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:124: multiple definition of 
`VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:123: multiple definition of 
`VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:121: multiple definition of `borderTol'; 
SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:119: multiple definition of 
`linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:117: multiple definition of 
`bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:225: multiple definition of `alignment'; 
SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:245: multiple definition of `factLUT'; 
SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:257: multiple definition of `clr'; 
SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:235: multiple definition of `div6'; 
SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:229: multiple definition of `rvLUT2'; 
SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:228: multiple definition of `rvLUT'; 
SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:227: multiple definition of `rv'; 
SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:142: multiple definition of `nofSamples'; 
SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:140: multiple definition of `nofTokens'; 
SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:138: multiple definition of `map'; 
SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:136: multiple definition of `mainTime0'; 
SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:128: multiple definition of `runName'; 
SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:126: multiple definition of 
`nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:125: multiple definition of `VCF_first_SNP'; 
SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:124: multiple definition of 
`VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:123: multiple definition of 
`VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:121: multiple definition of `borderTol'; 
SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:119: multiple definition of 
`linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:117: multiple definition of 
`bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:225: multiple definition of `alignment'; 
SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:257: multiple definition of `clr'; 
SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:245: multiple definition of `factLUT'; 
SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:228: multiple definition of `rvLUT'; 
SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:235: multiple definition of `div6'; 
SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:229: multiple definition of `rvLUT2'; 
SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:227: multiple definition of `rv'; 
SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:142: multiple definition of `nofSamples'; 
SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:140: multiple definition of `nofTokens'; 
SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:138: multiple definition of `map'; 
SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:136: multiple definition of `mainTime0'; 
SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:128: multiple definition of `runName'; 
SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:126: multiple definition of 
`nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:125: multiple definition of `VCF_first_SNP'; 
SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:124: multiple definition of 
`VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:123: multiple definition of 
`VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:121: multiple definition of `borderTol'; 
SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:119: multiple definition of 
`linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:117: multiple definition of 
`bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile.gcc:17: SweeD] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

--- End Message ---

--- Begin Message ---

Source: sweed
Source-Version: 3.2.1+dfsg-2
Done: =?utf-8?q?=C3=89tienne_Mollier?= <etienne.moll...@mailoo.org>

We believe that the bug you reported is fixed in the latest version of
sweed, 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.
Étienne Mollier <etienne.moll...@mailoo.org> (supplier of updated sweed 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: Wed, 22 Jul 2020 12:51:56 +0200
Source: sweed
Architecture: source
Version: 3.2.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <etienne.moll...@mailoo.org>
Closes: 957851
Changes:
 sweed (3.2.1+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Added gcc10.patch to fix compilation issues related with the move to GCC 10
     in Debian Bullseye.  (Closes: #957851)
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 13 (routine-update)
   * Add salsa-ci file (routine-update)
   * Rules-Requires-Root: no (routine-update)
   * Added repository information in debian/upstream/metadata
Checksums-Sha1:
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 29c110af8ab901d3c1352e09b1adf3b37dd911b5 4360 sweed_3.2.1+dfsg-2.debian.tar.xz
 b981db263866810f1207739a6e300fa2bd2ce0b6 5763 
sweed_3.2.1+dfsg-2_amd64.buildinfo
Checksums-Sha256:
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sweed_3.2.1+dfsg-2.dsc
 2387750a72c16b7b0e5c8c1a2b2a0d078a5acc0c45733533d04882afb00bdc8f 4360 
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 1a3ecb7ae6548ab555b05aec43e13498daf34e2a3ed21090033794a359d1f87f 5763 
sweed_3.2.1+dfsg-2_amd64.buildinfo
Files:
 ae01157b18012984f317f83c2e4a9611 1955 science optional sweed_3.2.1+dfsg-2.dsc
 62b677ef8d886ef850bd19b239e2e1fc 4360 science optional 
sweed_3.2.1+dfsg-2.debian.tar.xz
 5a9a4b0c4befa6e3a51628d2e7586eaa 5763 science optional 
sweed_3.2.1+dfsg-2_amd64.buildinfo

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--- End Message ---

Bug#957851: marked as done (sweed: ftbfs with GCC-10)

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