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author | Andrey Kislyuk <weaver@gentoo.org> | 2009-12-28 19:14:27 +0000 |
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committer | Andrey Kislyuk <weaver@gentoo.org> | 2009-12-28 19:14:27 +0000 |
commit | f8218a018f18966733b918caa5496973e813b7f5 (patch) | |
tree | 743d821088911b3dfbb3e0f42cf98146fcbf82f2 /sci-biology/glimmer | |
parent | ppc stable #296364 (diff) | |
download | historical-f8218a018f18966733b918caa5496973e813b7f5.tar.gz historical-f8218a018f18966733b918caa5496973e813b7f5.tar.bz2 historical-f8218a018f18966733b918caa5496973e813b7f5.zip |
QA fixes, including bug 298223
Package-Manager: portage-2.2_rc30/cvs/Linux x86_64
Diffstat (limited to 'sci-biology/glimmer')
-rw-r--r-- | sci-biology/glimmer/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/glimmer/Manifest | 5 | ||||
-rw-r--r-- | sci-biology/glimmer/files/glimmer-3.02-glibc210.patch | 24 | ||||
-rw-r--r-- | sci-biology/glimmer/glimmer-3.02-r1.ebuild | 29 |
4 files changed, 51 insertions, 13 deletions
diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog index 1dccf70808bd..5780aef0e1c4 100644 --- a/sci-biology/glimmer/ChangeLog +++ b/sci-biology/glimmer/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/glimmer # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.3 2009/01/04 01:24:22 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.4 2009/12/28 19:14:26 weaver Exp $ + + 28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild: + QA fixes, including bug 298223 *glimmer-3.02-r1 (04 Jan 2009) diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest index ab599ee58718..1d624ae15c5a 100644 --- a/sci-biology/glimmer/Manifest +++ b/sci-biology/glimmer/Manifest @@ -1,4 +1,5 @@ +AUX glimmer-3.02-glibc210.patch 799 RMD160 92e91e8ce9a39dd004152df712171052b726b0c5 SHA1 1a3f502692923f8b64e252c1b44f9ff68d343505 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 -EBUILD glimmer-3.02-r1.ebuild 1069 RMD160 a13e38d86cccb667c29551d56dcaec13e228c54e SHA1 79eef25e14c8f55507e1dbe332a3b3f47d5c82ff SHA256 4976d80b9bde54c5947801a52f7e2f669cb7d9677ca1c103966776e02409d1b6 -MISC ChangeLog 631 RMD160 d3cd14428f1ae35748a80a3352044a18c7cc64f7 SHA1 e314eb9e1245c79e732f3defb2816c90b1d4b98f SHA256 ceebaa6e5d381f8719d99813606293659530338e3dcdeaca7fb1eb5342e2326e +EBUILD glimmer-3.02-r1.ebuild 1273 RMD160 f0b6622a628940640c68dd58c754337c7786dfa9 SHA1 3a823ab62692ca8ffb5f2a93aff26c2a16481a7c SHA256 5762df4618f5d7b3b7fda91a8bd08a4befbeb82b9ecfdd927c0fc11072c1d0e2 +MISC ChangeLog 777 RMD160 308b1feed975657cc8d36c032551ebe353e7c950 SHA1 807ccd6b4e7c7215cb96f3475a815e4b6d58a27e SHA256 5eb0b481eed6d314921f0ad57c1ddc987839c1753ca1dc9c7f7ce734fb6aefd5 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch new file mode 100644 index 000000000000..f6051ec82054 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch @@ -0,0 +1,24 @@ +diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc +--- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 +@@ -443,7 +443,7 @@ + // Return a subscript corresponding to character ch . + + { +- char * p; ++ const char * p; + + p = strchr (CONVERSION_STRING, tolower (ch)); + if (p == NULL) +diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc +--- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 +@@ -1981,7 +1981,7 @@ + // model) for character ch . + + { +- char * p; ++ const char * p; + + p = strchr (ALPHA_STRING, tolower (Filter (ch))); + if (p == NULL) diff --git a/sci-biology/glimmer/glimmer-3.02-r1.ebuild b/sci-biology/glimmer/glimmer-3.02-r1.ebuild index d83c29e0e9a4..8a65fc316036 100644 --- a/sci-biology/glimmer/glimmer-3.02-r1.ebuild +++ b/sci-biology/glimmer/glimmer-3.02-r1.ebuild @@ -1,10 +1,12 @@ # Copyright 1999-2009 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.1 2009/01/04 01:24:22 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.2 2009/12/28 19:14:26 weaver Exp $ -inherit versionator +EAPI="2" -MY_PV=$(delete_all_version_separators) +inherit eutils + +MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" @@ -16,26 +18,33 @@ IUSE="" KEYWORDS="~amd64 ~x86" DEPEND="" -RDEPEND="!app-crypt/pkcrack +RDEPEND="app-shells/tcsh + !app-crypt/pkcrack !media-libs/libextractor" S="${WORKDIR}/${PN}${PV}" -src_compile() { +src_prepare() { sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" - sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh - cd src - emake || die "emake failed" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + epatch "${FILESDIR}/${PN}-${PV}-glibc210.patch" +} + +src_compile() { + emake -C src || die } src_install() { rm bin/test - dobin bin/* + dobin bin/* || die dodir /usr/share/${PN}/scripts insinto /usr/share/${PN}/scripts - doins scripts/* + doins scripts/* || die dodoc glim302notes.pdf } |