Bug 217921

Summary:	sci-biology/amap-2.1 fails w/ gcc-4.3.0; bump and patch
Product:	Gentoo Linux	Reporter:	Peter Alfredsen (RETIRED) <loki_val>
Component:	[OLD] GCC Porting	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	198121
Attachments:	amap-2.1--2.2.ebuild.patch 2.2-fix-cxxflags.patch 2.2-gcc43.patch

Description Peter Alfredsen (RETIRED) gentoo-dev

2008-04-16 10:14:33 UTC

i686-pc-linux-gnu-g++ -O2 -march=i686 -mtune=athlon-xp -msse -mmmx -pipe -ggdb3 -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.1"' -lm -o amap Amap.cc
In file included from Amap.cc:9:
MultiSequenceDag.h: In member function ‘MultiSequence* MultiSequenceDag::AlignDag(const SafeVector<SafeVector<SparseMatrix*> >&, float, bool, bool, bool, float)’:
MultiSequenceDag.h:780: error: ‘numeric_limits’ is not a member of ‘std’
MultiSequenceDag.h:780: error: expected primary-expression before ‘float’
MultiSequenceDag.h:780: error: expected `;' before ‘float’
Amap.cc: In function ‘bool GetInteger(char*, int*)’:
Amap.cc:618: error: ‘LONG_MAX’ was not declared in this scope
Amap.cc:618: error: ‘LONG_MIN’ was not declared in this scope
Amap.cc:619: error: ‘INT_MIN’ was not declared in this scope
Amap.cc:619: error: ‘INT_MAX’ was not declared in this scope
Amap.cc: In function ‘SafeVector<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > ParseParams(int, char**)’:
Amap.cc:748: error: ‘strcmp’ was not declared in this scope
make: *** [amap] Error 1


Reproducible: Always

Comment 1 Peter Alfredsen (RETIRED) gentoo-dev

2008-04-16 10:16:23 UTC

Created attachment 149913 [details, diff]
amap-2.1--2.2.ebuild.patch

Comment 2 Peter Alfredsen (RETIRED) gentoo-dev

2008-04-16 10:17:03 UTC

Created attachment 149914 [details, diff]
2.2-fix-cxxflags.patch

Comment 3 Peter Alfredsen (RETIRED) gentoo-dev

2008-04-16 10:17:23 UTC

Created attachment 149916 [details, diff]
2.2-gcc43.patch

Comment 4 Markus Dittrich (RETIRED) gentoo-dev

2008-04-17 18:21:06 UTC

Fixed in cvs. Thanks much for the patches.

cheers,
Markus