Your message dated Wed, 27 Jan 2016 13:24:28 +0000
with message-id <e1aoq5e-00045s...@franck.debian.org>
and subject line Bug#812681: fixed in mira 4.9.5-3
has caused the Debian Bug report #812681,
regarding mira: FTBFS with flex >= 2.6
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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--
812681: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812681
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: mira
Version: 4.9.5-2
Severity: serious
Usertags: goto-cc
During a rebuild of all Debian packages in a clean sid chroot (using cowbuilder
and pbuilder) the build failed with the following error. It should be noted
right away that this may be one of first attempts building with flex 2.6.
Notably, the flex NEWS says:
"C++ scanners now use references instead of pointers. See the manual for
details."
[...]
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.9.5_2\" -DPACKAGE_STRING=\"mira\ 4.9.5_2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.9.5_2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1
-DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1
-DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1
-DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src
-Wdate-time -DPUBLICQUIET -DAJ_Linux64 -g -O0 -fstack-protector-strong
-Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread
-I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -Werror=unused-value -std=c++14 -c -o exp_flexer.o
exp_flexer.cc
exp_flexer.cc: In member function 'virtual int EXPFlexLexer::yylex()':
exp_flexer.cc:766:9: error: no match for 'operator=' (operand types are
'std::istream {aka std::basic_istream<char>}' and 'std::istream* {aka
std::basic_istream<char>*}')
yyin = & std::cin;
^
In file included from /usr/include/c++/5/iostream:40:0,
from exp_flexer.cc:96:
/usr/include/c++/5/istream:625:7: note: candidate: std::basic_istream<_CharT,
_Traits>& std::basic_istream<_CharT,
_Traits>::operator=(std::basic_istream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_istream&& __rhs)
^
/usr/include/c++/5/istream:625:7: note: no known conversion for argument 1
from 'std::istream* {aka std::basic_istream<char>*}' to
'std::basic_istream<char>&&'
exp_flexer.cc:769:10: error: no match for 'operator=' (operand types are
'std::ostream {aka std::basic_ostream<char>}' and 'std::ostream* {aka
std::basic_ostream<char>*}')
yyout = & std::cout;
^
In file included from /usr/include/c++/5/iostream:39:0,
from exp_flexer.cc:96:
/usr/include/c++/5/ostream:402:7: note: candidate: std::basic_ostream<_CharT,
_Traits>& std::basic_ostream<_CharT,
_Traits>::operator=(std::basic_ostream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_ostream&& __rhs)
^
/usr/include/c++/5/ostream:402:7: note: no known conversion for argument 1
from 'std::ostream* {aka std::basic_ostream<char>*}' to
'std::basic_ostream<char>&&'
exp_flexer.cc:1260:44: error: cannot convert 'std::istream {aka
std::basic_istream<char>}' to 'std::istream* {aka std::basic_istream<char>*}'
in assignment
YY_CURRENT_BUFFER_LVALUE->yy_input_file = yyin;
^
In file included from /usr/include/c++/5/iostream:40:0,
from exp_flexer.cc:96:
/usr/include/c++/5/istream: In constructor
'EXPFlexLexer::EXPFlexLexer(std::istream*, std::ostream*)':
/usr/include/c++/5/istream:606:7: error: 'std::basic_istream<_CharT,
_Traits>::basic_istream() [with _CharT = char; _Traits =
std::char_traits<char>]' is protected
basic_istream()
^
exp_flexer.cc:1370:75: error: within this context
yyFlexLexer::yyFlexLexer( std::istream* arg_yyin, std::ostream* arg_yyout )
^
In file included from /usr/include/c++/5/iostream:39:0,
from exp_flexer.cc:96:
/usr/include/c++/5/ostream:384:7: error: 'std::basic_ostream<_CharT,
_Traits>::basic_ostream() [with _CharT = char; _Traits =
std::char_traits<char>]' is protected
basic_ostream()
^
exp_flexer.cc:1370:75: error: within this context
yyFlexLexer::yyFlexLexer( std::istream* arg_yyin, std::ostream* arg_yyout )
^
exp_flexer.cc:1372:7: error: no match for 'operator=' (operand types are
'std::istream {aka std::basic_istream<char>}' and 'std::istream* {aka
std::basic_istream<char>*}')
yyin = arg_yyin;
^
In file included from /usr/include/c++/5/iostream:40:0,
from exp_flexer.cc:96:
/usr/include/c++/5/istream:625:7: note: candidate: std::basic_istream<_CharT,
_Traits>& std::basic_istream<_CharT,
_Traits>::operator=(std::basic_istream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_istream&& __rhs)
^
/usr/include/c++/5/istream:625:7: note: no known conversion for argument 1
from 'std::istream* {aka std::basic_istream<char>*}' to
'std::basic_istream<char>&&'
exp_flexer.cc:1373:8: error: no match for 'operator=' (operand types are
'std::ostream {aka std::basic_ostream<char>}' and 'std::ostream* {aka
std::basic_ostream<char>*}')
yyout = arg_yyout;
^
In file included from /usr/include/c++/5/iostream:39:0,
from exp_flexer.cc:96:
/usr/include/c++/5/ostream:402:7: note: candidate: std::basic_ostream<_CharT,
_Traits>& std::basic_ostream<_CharT,
_Traits>::operator=(std::basic_ostream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_ostream&& __rhs)
^
/usr/include/c++/5/ostream:402:7: note: no known conversion for argument 1
from 'std::ostream* {aka std::basic_ostream<char>*}' to
'std::basic_ostream<char>&&'
exp_flexer.cc: In member function 'virtual void
EXPFlexLexer::switch_streams(std::istream*, std::ostream*)':
exp_flexer.cc:1419:9: error: no match for 'operator=' (operand types are
'std::ostream {aka std::basic_ostream<char>}' and 'std::ostream* {aka
std::basic_ostream<char>*}')
yyout = new_out;
^
In file included from /usr/include/c++/5/iostream:39:0,
from exp_flexer.cc:96:
/usr/include/c++/5/ostream:402:7: note: candidate: std::basic_ostream<_CharT,
_Traits>& std::basic_ostream<_CharT,
_Traits>::operator=(std::basic_ostream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_ostream&& __rhs)
^
/usr/include/c++/5/ostream:402:7: note: no known conversion for argument 1
from 'std::ostream* {aka std::basic_ostream<char>*}' to
'std::basic_ostream<char>&&'
exp_flexer.cc: In member function 'virtual int EXPFlexLexer::LexerInput(char*,
int)':
exp_flexer.cc:1428:11: error: base operand of '->' has non-pointer type
'std::istream {aka std::basic_istream<char>}'
if ( yyin->eof() || yyin->fail() )
^
exp_flexer.cc:1428:26: error: base operand of '->' has non-pointer type
'std::istream {aka std::basic_istream<char>}'
if ( yyin->eof() || yyin->fail() )
^
exp_flexer.cc:1432:6: error: base operand of '->' has non-pointer type
'std::istream {aka std::basic_istream<char>}'
yyin->get( buf[0] );
^
exp_flexer.cc:1434:11: error: base operand of '->' has non-pointer type
'std::istream {aka std::basic_istream<char>}'
if ( yyin->eof() )
^
exp_flexer.cc:1437:11: error: base operand of '->' has non-pointer type
'std::istream {aka std::basic_istream<char>}'
if ( yyin->bad() )
^
exp_flexer.cc: In member function 'virtual void EXPFlexLexer::LexerOutput(const
char*, int)':
exp_flexer.cc:1454:14: error: base operand of '->' has non-pointer type
'std::ostream {aka std::basic_ostream<char>}'
(void) yyout->write( buf, size );
^
exp_flexer.cc: In member function 'virtual void
EXPFlexLexer::yyrestart(std::istream*)':
exp_flexer.cc:1774:48: error: no matching function for call to
'EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream*&)'
yy_init_buffer( YY_CURRENT_BUFFER, input_file );
^
In file included from exp_flexer.cc:323:0:
/usr/include/FlexLexer.h:160:7: note: candidate: void
EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
void yy_init_buffer( struct yy_buffer_state* b, FLEX_STD istream& s );
^
/usr/include/FlexLexer.h:160:7: note: no known conversion for argument 2 from
'std::istream* {aka std::basic_istream<char>*}' to 'std::istream& {aka
std::basic_istream<char>&}'
exp_flexer.cc: In member function 'void EXPFlexLexer::yy_load_buffer_state()':
exp_flexer.cc:1817:7: error: no match for 'operator=' (operand types are
'std::istream {aka std::basic_istream<char>}' and 'std::istream* {aka
std::basic_istream<char>*}')
yyin = YY_CURRENT_BUFFER_LVALUE->yy_input_file;
^
In file included from /usr/include/c++/5/iostream:40:0,
from exp_flexer.cc:96:
/usr/include/c++/5/istream:625:7: note: candidate: std::basic_istream<_CharT,
_Traits>& std::basic_istream<_CharT,
_Traits>::operator=(std::basic_istream<_CharT, _Traits>&&) [with _CharT = char;
_Traits = std::char_traits<char>]
operator=(basic_istream&& __rhs)
^
/usr/include/c++/5/istream:625:7: note: no known conversion for argument 1
from 'std::istream* {aka std::basic_istream<char>*}' to
'std::basic_istream<char>&&'
exp_flexer.cc: In member function 'virtual yy_buffer_state*
EXPFlexLexer::yy_create_buffer(std::istream*, int)':
exp_flexer.cc:1846:26: error: no matching function for call to
'EXPFlexLexer::yy_init_buffer(yy_buffer_state*&, std::istream*&)'
yy_init_buffer( b, file );
^
In file included from exp_flexer.cc:323:0:
/usr/include/FlexLexer.h:160:7: note: candidate: void
EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
void yy_init_buffer( struct yy_buffer_state* b, FLEX_STD istream& s );
^
/usr/include/FlexLexer.h:160:7: note: no known conversion for argument 2 from
'std::istream* {aka std::basic_istream<char>*}' to 'std::istream& {aka
std::basic_istream<char>&}'
exp_flexer.cc: At global scope:
exp_flexer.cc:23:25: error: prototype for 'void
EXPFlexLexer::yy_init_buffer(YY_BUFFER_STATE, std::istream*)' does not match
any in class 'EXPFlexLexer'
#define yyFlexLexer EXPFlexLexer
^
exp_flexer.cc:1876:10: note: in expansion of macro 'yyFlexLexer'
void yyFlexLexer::yy_init_buffer( YY_BUFFER_STATE b, std::istream* file )
^
In file included from exp_flexer.cc:323:0:
/usr/include/FlexLexer.h:160:7: error: candidate is: void
EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
void yy_init_buffer( struct yy_buffer_state* b, FLEX_STD istream& s );
^
Makefile:482: recipe for target 'exp_flexer.o' failed
make[7]: *** [exp_flexer.o] Error 1
The full build log is attached; please do let me know if the problem is
unreproducible, in which case I shall try to investigate further.
Best,
Michael
mira-build-log.txt.gz
Description: application/gunzip
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: mira
Source-Version: 4.9.5-3
We believe that the bug you reported is fixed in the latest version of
mira, 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 812...@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 mira 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: Wed, 27 Jan 2016 13:19:53 +0100
Source: mira
Binary: mira-assembler mira-examples mira-doc
Architecture: source amd64 all
Version: 4.9.5-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
mira-assembler - Whole Genome Shotgun and EST Sequence Assembler
mira-doc - documentation for the mira assembler
mira-examples - files to experiment with the mira assembler
Closes: 812681
Changes:
mira (4.9.5-3) unstable; urgency=medium
.
* Remove *.cc files that are created by old flex version which breaks
build otherwise
Closes: #812681
Checksums-Sha1:
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ad226b0fed9d3ad4ac3ecd8b9fc766c7f881d748 14880 mira_4.9.5-3.debian.tar.xz
de85a67be290e5a7df2e3c59a88f45612f704b11 22426622
mira-assembler-dbgsym_4.9.5-3_amd64.deb
46a1ff42b7710efd01a8c98310c640742390ecce 1797462
mira-assembler_4.9.5-3_amd64.deb
4056d6264ba2c5d0effba977ad8ec4696319b680 2787998 mira-doc_4.9.5-3_all.deb
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Checksums-Sha256:
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mira_4.9.5-3.dsc
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mira-assembler-dbgsym_4.9.5-3_amd64.deb
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mira-assembler_4.9.5-3_amd64.deb
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Files:
b3b7dd2098d568f4228dcf566f82fe3c 2362 science optional mira_4.9.5-3.dsc
07e070ae56411ee551db5b9b32077195 14880 science optional
mira_4.9.5-3.debian.tar.xz
7f6ff071e2df2fe37b51f07c930a62bd 22426622 debug extra
mira-assembler-dbgsym_4.9.5-3_amd64.deb
6884a5962f74ab964e533348b6ac32d9 1797462 science optional
mira-assembler_4.9.5-3_amd64.deb
6a7c4104afc0b86f0cbbec724b1a866e 2787998 doc optional mira-doc_4.9.5-3_all.deb
2e7555a99674aeca549466ce7a5363a9 6567882 science optional
mira-examples_4.9.5-3_all.deb
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