Your message dated Fri, 17 Apr 2020 20:39:19 +0000
with message-id <[email protected]>
and subject line Bug#957683: fixed in phyx 1.01+ds-2
has caused the Debian Bug report #957683,
regarding phyx: 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
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immediately.)
--
957683: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957683
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:phyx
Version: 1.01+ds-1
Severity: normal
Tags: sid bullseye
User: [email protected]
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/phyx_1.01+ds-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
[...]
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "edlib.d"
-o "edlib.o" "edlib.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_nw.d"
-o "main_nw.o" "main_nw.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_sw.d"
-o "main_sw.o" "main_sw.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"seq_sample.d" -o "seq_sample.o" "seq_sample.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_boot.d" -o "main_boot.o" "main_boot.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "concat.d"
-o "concat.o" "concat.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_concat.d" -o "main_concat.o" "main_concat.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "sstat.d"
-o "sstat.o" "sstat.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_sstat.d" -o "main_sstat.o" "main_sstat.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "recode.d"
-o "recode.o" "recode.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_recode.d" -o "main_recode.o" "main_recode.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_bp.d"
-o "main_bp.o" "main_bp.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_t2new.d" -o "main_t2new.o" "main_t2new.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "main_rr.d"
-o "main_rr.o" "main_rr.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d"
-o "aa2cdn.o" "aa2cdn.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF
"main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp"
g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "tlate.d"
-o "tlate.o" "tlate.cpp"
In file included from tlate.cpp:13:
tlate.h:17:10: error: ‘string’ was not declared in this scope
17 | map <string, string> table_;
| ^~~~~~
tlate.h:1:1: note: ‘std::string’ is defined in header ‘<string>’; did you
forget to ‘#include <string>’?
+++ |+#include <string>
1 | /*
tlate.h:17:18: error: ‘string’ was not declared in this scope
17 | map <string, string> table_;
| ^~~~~~
tlate.h:17:18: note: ‘std::string’ is defined in header ‘<string>’; did you
forget to ‘#include <string>’?
tlate.h:17:24: error: template argument 1 is invalid
17 | map <string, string> table_;
| ^
tlate.h:17:24: error: template argument 2 is invalid
tlate.h:17:24: error: template argument 3 is invalid
tlate.h:17:24: error: template argument 4 is invalid
tlate.h:20:18: error: expected ‘)’ before ‘const’
20 | TLATE (string const& table);
| ~ ^~~~~~
| )
tlate.h:21:5: error: ‘string’ does not name a type; did you mean ‘stdin’?
21 | string translate (string& dna);
| ^~~~~~
| stdin
tlate.cpp:292:8: error: no declaration matches ‘std::string
TLATE::translate(std::string&)’
292 | string TLATE::translate (string& dna) {
| ^~~~~
tlate.cpp:292:8: note: no functions named ‘std::string
TLATE::translate(std::string&)’
In file included from tlate.cpp:13:
tlate.h:15:7: note: ‘class TLATE’ defined here
15 | class TLATE {
| ^~~~~
tlate.cpp:314:1: error: no declaration matches ‘TLATE::TLATE(const string&)’
314 | TLATE::TLATE (string const& table) {
| ^~~~~
In file included from tlate.cpp:13:
tlate.h:15:7: note: candidates are: ‘constexpr TLATE::TLATE(TLATE&&)’
15 | class TLATE {
| ^~~~~
tlate.h:15:7: note: ‘constexpr TLATE::TLATE(const TLATE&)’
tlate.h:15:7: note: ‘TLATE::TLATE()’
tlate.h:15:7: note: ‘class TLATE’ defined here
make[1]: *** [Makefile:334: tlate.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j4 returned exit code 2
make: *** [debian/rules:9: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: phyx
Source-Version: 1.01+ds-2
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
phyx, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated phyx 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 17 Apr 2020 21:56:19 +0200
Source: phyx
Architecture: source
Version: 1.01+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 957683
Changes:
phyx (1.01+ds-2) unstable; urgency=medium
.
* Team upload
.
[ Nilesh Patra ]
* Add patch to build with g++-10
Closes: #957683
.
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* debian/copyright: use spaces rather than tabs to start continuation
lines.
* Set upstream metadata fields: Bug-Database, Bug-Submit.
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--- End Message ---
