Bug 393311

Summary:	sci-biology/emboss-6.0.1 does not respect CFLAGS="-O?"
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	New packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED OBSOLETE
Severity:	minor	CC:	jlec, mmokrejs
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	emboss-6.3.1_p4-r1.ebuild.patch

Description Agostino Sarubbo gentoo-dev

2011-12-05 19:53:12 UTC

x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -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 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I../plplot -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -march=native -O2 -g0 -O2 -D__amd64__ -MT embdmx.lo -MD -MP -MF .deps/embdmx.Tpo -c embdmx.c -o embdmx.o >/dev/null 2>&1
 x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -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 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I../plplot -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -march=native -O2 -g0 -O2 -D__amd64__ -MT embdomain.lo -MD -MP -MF .deps/embdomain.Tpo -c embdomain.c  -fPIC -DPIC -o .libs/embdomain.o


amd64box ~ # emerge --info | grep CFLA
CFLAGS="-march=native -O2 -g0"

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2011-12-05 19:58:43 UTC

prosite is a db. All files included are:


prosite-20.72/
prosite-20.72/prosite.doc
prosite-20.72/unirule.pdf
prosite-20.72/prosite.dat
prosite-20.72/prorule.dat

How do you compile code here?

Comment 2 Martin Mokrejš 2012-02-02 17:39:58 UTC

Created attachment 300775 [details, diff]
emboss-6.3.1_p4-r1.ebuild.patch

This patch works for me. Tested with:

CFLAGS="-ggdb -pipe -march=native" emerge emboss

Comment 3 Justin Lecher (RETIRED) gentoo-dev

2015-08-27 13:50:46 UTC

commit 08fae0a30263fd06fe51ac5b75301d574be9e1be
Author: Justin Lecher <jlec@gentoo.org>
Date:   Thu Aug 27 15:47:31 2015 +0200
    
    sci-biology/emboss: Drop old
    
    obsolets multiple bugs
    
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443
    
    Package-Manager: portage-2.2.20.1
    Signed-off-by: Justin Lecher <jlec@gentoo.org>
    
    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08fae0a30263fd06fe51ac5b75301d574be9e1be