Your message dated Sat, 05 Mar 2016 18:30:56 +0000
with message-id <[email protected]>
and subject line Bug#811615: fixed in rsem 1.2.26+dfsg-2
has caused the Debian Bug report #811615,
regarding FTBFS with GCC 6: cannot convert x to y
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
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
811615: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811615
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: rsem
Version: 1.2.23+dfsg-1
Severity: important
User: [email protected]
Usertags: ftbfs-gcc-6 gcc-6-cannot-convert
This package fails to build with GCC 6. GCC 6 has not been released
yet, but it's expected that GCC 6 will become the default compiler for
stretch.
Note that only the first error is reported; there might be more. You
can find a snapshot of GCC 6 in experimental. To build with GCC 6,
you can set CC=gcc-6 CXX=g++-6 explicitly.
> sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
> g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
> -Werror=format-security -Wl,-z,relro -O3 -Wall scanForPairedEndReads.cpp
> /usr/lib/libbam.a -lz -lpthread -o rsem-scan-for-paired-end-reads
> buildReadIndex.cpp: In function 'void buildIndex(char*, int, bool)':
> buildReadIndex.cpp:38:32: error: cannot convert 'std::basic_istream<char>' to
> 'bool' in assignment
> success = (getline(fin, line));
> ^
>
> buildReadIndex.cpp:40:32: error: cannot convert 'std::basic_istream<char>' to
> 'bool' in assignment
> success = (getline(fin, line));
> ^
>
> buildReadIndex.cpp:44:33: error: cannot convert 'std::basic_istream<char>' to
> 'bool' in assignment
> success = (getline(fin, line));
> ^
>
> buildReadIndex.cpp:46:33: error: cannot convert 'std::basic_istream<char>' to
> 'bool' in assignment
> success = (getline(fin, line));
> ^
>
> Makefile:59: recipe for target 'rsem-build-read-index' failed
> make[2]: *** [rsem-build-read-index] Error 1
> make[2]: *** Waiting for unfinished jobs....
> In file included from getUnique.cpp:12:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
> static bool verbose = true; // show detail intermediate outputs
> ^~~~~~~
>
> In file included from wiggle.cpp:10:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
> static bool verbose = true; // show detail intermediate outputs
> ^~~~~~~
>
> In file included from samValidator.cpp:12:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
> static bool verbose = true; // show detail intermediate outputs
> ^~~~~~~
>
> In file included from parseIt.cpp:22:0:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos);
> ^
>
> In file included from parseIt.cpp:23:0:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos>>insertL);
> ^
>
> In file included from scanForPairedEndReads.cpp:13:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
> static bool verbose = true; // show detail intermediate outputs
> ^~~~~~~
>
> Makefile:55: recipe for target 'parseIt.o' failed
> make[2]: *** [parseIt.o] Error 1
> In file included from tbam2gbam.cpp:5:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
> static bool verbose = true; // show detail intermediate outputs
> ^~~~~~~
>
> In file included from EM.cpp:24:0:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos);
> ^
>
> In file included from EM.cpp:25:0:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos>>insertL);
> ^
>
> In file included from SingleModel.h:26:0,
> from simulation.cpp:22:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos);
> ^
>
> In file included from PairedEndModel.h:27:0,
> from simulation.cpp:24:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos>>insertL);
> ^
>
> In file included from SingleModel.h:26:0,
> from Gibbs.cpp:15:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos);
> ^
>
> In file included from SingleModel.h:26:0,
> from calcCI.cpp:16:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos);
> ^
>
> In file included from PairedEndModel.h:27:0,
> from Gibbs.cpp:17:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos>>insertL);
> ^
>
> In file included from PairedEndModel.h:27:0,
> from calcCI.cpp:18:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert
> 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to
> 'bool' in return
> return (in>>sid>>pos>>insertL);
> ^
>
> Makefile:104: recipe for target 'simulation.o' failed
> make[2]: *** [simulation.o] Error 1
> Makefile:111: recipe for target 'Gibbs.o' failed
> make[2]: *** [Gibbs.o] Error 1
> Makefile:120: recipe for target 'calcCI.o' failed
> make[2]: *** [calcCI.o] Error 1
> Makefile:84: recipe for target 'EM.o' failed
> make[2]: *** [EM.o] Error 1
--
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise
--- End Message ---
--- Begin Message ---
Source: rsem
Source-Version: 1.2.26+dfsg-2
We believe that the bug you reported is fixed in the latest version of
rsem, 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.
Michael R. Crusoe <[email protected]> (supplier of updated rsem 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: Sat, 05 Mar 2016 05:27:01 -0800
Source: rsem
Binary: rsem
Architecture: source
Version: 1.2.26+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Description:
rsem - RNA-Seq by Expectation-Maximization
Closes: 811615
Changes:
rsem (1.2.26+dfsg-2) unstable; urgency=medium
.
* Now compatible with g++-6 (Closes: #811615)
* Section set to 'extra' due to dependency on bowtie|bowtie2 which are both
in section 'extra'.
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