Your message dated Fri, 22 Oct 2021 16:49:05 +0000
with message-id <e1mdxj7-000bpd...@fasolo.debian.org>
and subject line Bug#984036: fixed in disulfinder 1.2.11-11
has caused the Debian Bug report #984036,
regarding disulfinder: ftbfs with GCC-11
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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--
984036: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984036
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:disulfinder
Version: 1.2.11-10
Severity: normal
Tags: sid bookworm
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye release]
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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/disulfinder_1.2.11-10_unstable_gcc11.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
from Input/createBRNNDataset.h:1,
from Input/createBRNNDataset.cpp:2:
Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used
[-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used
[-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as
ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: ‘aa_codes’ defined but not used
[-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered
in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o
In file included from Input/utils.h:2,
from Input/createKernelDataset.h:1,
from Input/createKernelDataset.cpp:2:
Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used
[-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used
[-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as
ordered in tdb profile files
| ^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o
Output/makeHTMLOutput.cpp: In function ‘void makeHTMLOutput(std::string, const
char*, int, std::string, std::ostream&)’:
Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string
constant to ‘char*’ [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~~
Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string
constant to ‘char*’ [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o
Output/makeASCIIOutput.cpp: In function ‘void makeASCIIOutput(std::string,
const char*, int, std::string, std::ostream&)’:
Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string
constant to ‘char*’ [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~~
Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string
constant to ‘char*’ [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o
FSA-Alignment/viterbi_aligner.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c NN/array.cpp -o NN/array.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o
In file included from BRNN/RNNs/Node.h:4,
from BRNN/RNNs/Node.cpp:4:
BRNN/RNNs/Options.h:69:5: error: ISO C++17 does not allow dynamic exception
specifications
69 | throw(BadOptionSetting);
| ^~~~~
BRNN/RNNs/Options.h:143:5: error: ISO C++17 does not allow dynamic exception
specifications
143 | throw(BadOptionSetting);
| ^~~~~
BRNN/RNNs/Options.h:180:5: error: ISO C++17 does not allow dynamic exception
specifications
180 | throw(BadOptionSetting);
| ^~~~~
make[3]: *** [Makefile:48: BRNN/RNNs/Node.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src'
make[2]: *** [Makefile:24: disulfinder] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" returned
exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: disulfinder
Source-Version: 1.2.11-11
Done: Nilesh Patra <nil...@debian.org>
We believe that the bug you reported is fixed in the latest version of
disulfinder, 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 984...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@debian.org> (supplier of updated disulfinder 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: SHA512
Format: 1.8
Date: Fri, 22 Oct 2021 21:59:19 +0530
Source: disulfinder
Architecture: source
Version: 1.2.11-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@debian.org>
Closes: 984036
Changes:
disulfinder (1.2.11-11) unstable; urgency=medium
.
* Team Upload.
* d/rules: Force -std=c++14 (Closes: #984036)
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--- End Message ---
