Your message dated Thu, 04 Aug 2022 11:05:25 +0000
with message-id <e1ojyfn-004jdg...@fasolo.debian.org>
and subject line Bug#1016281: fixed in pirs 2.0.2+dfsg-11
has caused the Debian Bug report #1016281,
regarding pirs: FTBFS: pirs_diploid.cpp:322:34: error: ‘time’ was not declared
in this scope
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.
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--
1016281: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016281
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: pirs
Version: 2.0.2+dfsg-10
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20220728 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time
> -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -c -o Profile.o Profile.cpp
> InputStream.h: In constructor ‘InputStream::InputStream(const char*)’:
> InputStream.h:54:23: warning: ‘void* memset(void*, int, size_t)’ clearing an
> object of non-trivial type ‘class InputStream’; use assignment or
> value-initialization instead [-Wclass-memaccess]
> 54 | memset(this, 0, sizeof(*this));
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
> InputStream.h:25:7: note: ‘class InputStream’ declared here
> 25 | class InputStream {
> | ^~~~~~~~~~~
> In file included from pirs_diploid.cpp:12:
> OutputStream.h: In constructor ‘OutputStream::OutputStream()’:
> OutputStream.h:54:23: warning: ‘void* memset(void*, int, size_t)’ clearing an
> object of non-trivial type ‘class OutputStream’; use assignment or
> value-initialization instead [-Wclass-memaccess]
> 54 | memset(this, 0, sizeof(*this));
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
> OutputStream.h:33:7: note: ‘class OutputStream’ declared here
> 33 | class OutputStream {
> | ^~~~~~~~~~~~
> OutputStream.h: In constructor ‘OutputStream::OutputStream(const char*,
> OutputType)’:
> OutputStream.h:58:23: warning: ‘void* memset(void*, int, size_t)’ clearing an
> object of non-trivial type ‘class OutputStream’; use assignment or
> value-initialization instead [-Wclass-memaccess]
> 58 | memset(this, 0, sizeof(*this));
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
> OutputStream.h:33:7: note: ‘class OutputStream’ declared here
> 33 | class OutputStream {
> | ^~~~~~~~~~~~
> pirs_diploid.cpp: In function ‘void pirs_diploid_parse_command_line(int,
> char**)’:
> pirs_diploid.cpp:322:34: error: ‘time’ was not declared in this scope
> 322 | seed = (uint64_t)time(NULL) * (uint64_t)getpid();
> | ^~~~
> pirs_diploid.cpp:13:1: note: ‘time’ is defined in header ‘<ctime>’; did you
> forget to ‘#include <ctime>’?
> 12 | #include "OutputStream.h"
> +++ |+#include <ctime>
> 13 |
> g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time
> -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp
> pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a
> space between literal and string macro [-Wliteral-suffix]
> 168 | " "DEFAULT_BASE_CALLING_PROFILE"\n"
> | ^
> pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a
> space between literal and string macro [-Wliteral-suffix]
> 174 | " "DEFAULT_INDEL_PROFILE"\n"
> | ^
> pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a
> space between literal and string macro [-Wliteral-suffix]
> 180 | " "DEFAULT_GC_BIAS_PROFILE_100",\n"
> | ^
> pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a
> space between literal and string macro [-Wliteral-suffix]
> 181 | " "DEFAULT_GC_BIAS_PROFILE_150",\n"
> | ^
> pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a
> space between literal and string macro [-Wliteral-suffix]
> 182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n"
> | ^
> pirs_simulate.cpp:672:25: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n",
> | ^
> pirs_simulate.cpp:700:30: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 700 |
> info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t",
> | ^
> pirs_simulate.cpp:1235:38: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1235 | info("Simulated %"PRIu64" of
> %"PRIu64" read pairs\n",
> | ^
> pirs_simulate.cpp:1235:57: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1235 | info("Simulated %"PRIu64" of
> %"PRIu64" read pairs\n",
> | ^
> pirs_simulate.cpp:1540:35: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first,
> it->second);
> | ^
> pirs_simulate.cpp:1557:9: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1557 | "# The total number of read pairs that were simulated was
> %"PRIu64".\n"
> | ^
> pirs_simulate.cpp:1574:34: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1574 | error_log.printf("%d\t%"PRIu64"\t%g\n",
> | ^
> pirs_simulate.cpp:1579:26: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1579 | error_log.printf("total\t%"PRIu64"\t%g\n",
> | ^
> pirs_simulate.cpp:1685:33: warning: invalid suffix on literal; C++11 requires
> a space between literal and string macro [-Wliteral-suffix]
> 1685 | log_parameter(info_log, "Random seed:
> %"PRIu64"\n",
> | ^
> make[4]: *** [Makefile:518: pirs_diploid.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2022/07/28/pirs_2.0.2+dfsg-10_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220728;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220728&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: pirs
Source-Version: 2.0.2+dfsg-11
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pirs, 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 1016...@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 pirs 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: Thu, 04 Aug 2022 12:03:34 +0200
Source: pirs
Architecture: source
Version: 2.0.2+dfsg-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1016281
Changes:
pirs (2.0.2+dfsg-11) unstable; urgency=medium
.
* Standards-Version: 4.6.1 (routine-update)
* Fix error: ‘time’ was not declared in this scope
Closes: #1016281
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Files:
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ec84a3d5a2b4bb574d1c9e9c3fae75f8 7484 science optional
pirs_2.0.2+dfsg-11.debian.tar.xz
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pirs_2.0.2+dfsg-11_amd64.buildinfo
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--- End Message ---
