Summary: | sci-biology/emboss-6.0.1 with dev-libs/libpcre-8.35 - file collision in /usr/include/pcreposix.h /usr/include/pcre.h | ||
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Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED OBSOLETE | ||
Severity: | normal | CC: | jlec |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Toralf Förster
2015-01-03 09:12:00 UTC
Please try the science overlay, we have finally gotten around to fixing emboss and removed all bundled libraries (including pcre) and now link to system libraries. In future, all <sci-biology/emboss-6.6.0 ebuilds will eventually be removed. (In reply to Ted Tanberry from comment #1) > Please try the science overlay, we have finally gotten around to fixing > emboss and removed all bundled libraries (including pcre) and now link to > system libraries. In future, all <sci-biology/emboss-6.6.0 ebuilds will > eventually be removed. Hm, this is just a build bot chroot for the vanilla gentoo tree - so shall I exclude a category from it ? I think emboss-6.3.1_p4-r2 which used to be the last 6.3.1_p4 ebuild in the tree (sci overlay) should be restored and stabilized. It does not have this problem: # emerge -pv =sci-biology/emboss-6.3.1_p4-r2 ... Calculating dependencies... done! [ebuild R ] sci-biology/emboss-6.3.1_p4-r2::x-portage USE="-X -minimal* -mysql -pdf -png -postgres -static-libs" 0 KiB # # equery files emboss | grep -i pcre /usr/include/emboss/ajax-pcre-config.h # # grep -i pcre /usr/local/portage/sci-biology/emboss/files/* /usr/local/portage/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch: AC_SUBST(DEFINE_USE_SYSTEM_PCRE) ... From the above you can see it uses system-wide pcre. The patch does not actually chnagethat (no minus or plus sign at the beginning of the line). So, it should be the same also with previous _p4-r1 ebuild which was in the main tree. emboss-6.6.0 fixes all these issues, have you tried it? 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 |