[Debian-med-packaging] Bug#1016281: pirs: FTBFS: pirs_diploid.cpp:322:34: error: ‘time’ was not declared in this scope
Lucas Nussbaum
lucas at debian.org
Fri Jul 29 17:22:56 BST 2022
Source: pirs
Version: 2.0.2+dfsg-10
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220728&fusertaguser=lucas@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.
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