From 590b9b7b03bf4651e099949e318755af7cfa81b8 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 1 Aug 2021 22:03:23 +0100 Subject: gentoo resync : 01.08.2021 --- sci-biology/Manifest.gz | Bin 22141 -> 22146 bytes sci-biology/bowtie/Manifest | 7 +- sci-biology/bowtie/bowtie-2.2.9.ebuild | 61 --- sci-biology/bowtie/bowtie-2.4.4.ebuild | 55 +++ .../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 -- sci-biology/bowtie/metadata.xml | 19 +- sci-biology/emboss/Manifest | 7 +- sci-biology/emboss/emboss-6.6.0-r1.ebuild | 14 +- .../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch | 11 - .../files/emboss-6.6.0_fix-build-system.patch | 411 --------------------- .../files/emboss-6.6.0_plplot-declarations.patch | 61 --- .../emboss-6.6.0_qa-implicit-declarations.patch | 74 ---- 12 files changed, 76 insertions(+), 673 deletions(-) delete mode 100644 sci-biology/bowtie/bowtie-2.2.9.ebuild create mode 100644 sci-biology/bowtie/bowtie-2.4.4.ebuild delete mode 100644 sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch delete mode 100644 sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch delete mode 100644 sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch delete mode 100644 sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch delete mode 100644 sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 74a32cb73e6b..c2d8ff11cb80 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index f9a42acddbb3..c2958853f2a0 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,4 +1,3 @@ -AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5 -DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 -EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85 -MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301 +DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da +EBUILD bowtie-2.4.4.ebuild 1202 BLAKE2B 4ba725c1a324fcff1444451c51b0f5f3d031dc6bb1c0e20eef82de155c19d2bff504531fc8ce2821f6955cc97b0ab162ff8c28c8b651629bf2127c90e972ab96 SHA512 c3fd41634d8b32b389a196b6443d8768541afceb67ca404ade678be166af4624733fa4c2ee5ce5683db415a9fb1e70a7edeeadeee3e9d3905c09f70e512b4ffe +MISC metadata.xml 341 BLAKE2B 6128267ebf9a8b0b4b6abf9da19a57f9a1da5492a6c878a531e7c43dc139c614793c4919d1a4a99739dfee4a3e6861554b9155f46d7af60a2f998811890bb70a SHA512 02b50e247581f0454829e2aaca768cc8719ee181db276feb20c5b4ed3ab3ba820af8db491075906eeb7bb4e0941940e98c5ee81a8efae0b633881e8f14cbcd74 diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild deleted file mode 100644 index 0bacb8ca25d7..000000000000 --- a/sci-biology/bowtie/bowtie-2.2.9.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl - tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) -PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild b/sci-biology/bowtie/bowtie-2.4.4.ebuild new file mode 100644 index 000000000000..2ba75bc2bca7 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild @@ -0,0 +1,55 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) + +inherit python-single-r1 toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip" +S="${WORKDIR}/${PN}2-${PV}" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse2 examples" +REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/perl + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND="app-arch/unzip" + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + CXXFLAGS="" \ + CPPFLAGS="${CPPFLAGS}" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" +} + +src_install() { + dobin bowtie2 bowtie2-* + + exeinto /usr/libexec/bowtie2 + doexe scripts/* + + HTML_DOCS=( doc/{manual.html,style.css} ) + einstalldocs + dodoc TUTORIAL + newman MANUAL bowtie2.1 + + python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect} + + if use examples; then + docinto examples + dodoc -r example/. + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch deleted file mode 100644 index cd2a67b6a52b..000000000000 --- a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch +++ /dev/null @@ -1,29 +0,0 @@ -Fix building with C++14, which errors out due to differing semantics between C++98 -and C++14 with regards to allowing destructors to throw exceptions. -See also: https://bugs.gentoo.org/show_bug.cgi?id=593966 - ---- a/blockwise_sa.h -+++ b/blockwise_sa.h -@@ -87,7 +87,11 @@ - _logger(__logger) - { } - -- virtual ~BlockwiseSA() { } -+ virtual ~BlockwiseSA() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ { } - - /** - * Get the next suffix; compute the next bucket if necessary. -@@ -216,6 +220,9 @@ - { _randomSrc.init(__seed); reset(); } - - ~KarkkainenBlockwiseSA() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif - { - #ifdef WITH_TBB - tbb_grp.wait(); diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index 71e8d3bb8e0f..f570878c86e5 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -1,16 +1,11 @@ - - sci-biology@gentoo.org - Gentoo Biology Project - - - bowtie-bio - - - Enables building bowtie with the Intel - Threading Building Blocks from dev-cpp/tbb. This - flag is recommended. - + + sci-biology@gentoo.org + Gentoo Biology Project + + + bowtie-bio + diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index d3d3d46bb05a..192e7507fed5 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,8 +1,5 @@ AUX README.gentoo 1522 BLAKE2B 566213e78e6c74fc6c8745391fbdbc477c9d1793f74e68fb0465ba4f842203e1670dd6216c4181326a4ccbf0c051daa99a376a15dd5b0714473f84ed8404e8f7 SHA512 a5441a056ebb11d24b83b8bfb9182f0753b85ec5ba126a123eb97c55fc665dadff2cc5f16c8e4314535f1b6a206c200324c0c5d5db6af109c841ee68ac76bb07 -AUX emboss-6.6.0_FORTIFY_SOURCE-fix.patch 417 BLAKE2B 6662dae6877f28bc53942e3989846835721c31a79eeb62fd0b2fc4bf5bf8dc63c25f43831667985109f109bf463f795190018801ba84811c7e94b135047f7d4c SHA512 9873504675825613c913fbd8c03d919c5d70ad7f15e3983ae9dc5ecd04e57d1086c303a4f38efd29def4f089099b24449014bbe965816c7f8b37a5d4ffa13469 -AUX emboss-6.6.0_fix-build-system.patch 12599 BLAKE2B dbe6a94a801b0f46df0e7490c7b07ad85a143c07821d8bc083221d07b1286275c7fd5cd183c5c08d06dc6fb3c71eacd265d872647828991fd52551ae618bcaf7 SHA512 60dbb50967b0b855fabd68f2df7713da81007cb84aeb3f2d7510d13e533e3b19ed3d07e012010ebb1b2af04522f6f2142fbef405b9b580740a6bb5d30319b67b -AUX emboss-6.6.0_plplot-declarations.patch 1562 BLAKE2B f6c19e6cb7c2eb8110a3841ed566d81411e75a6898cdfbb8ce4754a69291f78a069a44fbc5027430611ee83ca5a7abe1e536a59bedd01e30227c5762622614bd SHA512 fc27b7c1d518b5cdacf1964d56219c6574f43d18dc324e41b9dcdfd1afef17a784f2b209b62c366fb902ba57a50f438a1b328eb2118ee9463ce82b36039bc0bb -AUX emboss-6.6.0_qa-implicit-declarations.patch 1324 BLAKE2B 42da02b30fa201e24091df762386a88ad76709d192dab95c82cf578126ef9973ba1e927711ac5dd3eee1cfac22a2d29fc75045ce72322cbd7faaa6d50564319e SHA512 15c303fe48a438f50f1c9a0efd7e8fcbcb4102151fc182feb8e0d74c47c3435385a1e44436cebd3c2017c97dd89b82832258748f28f3740e511a92b088f539fb DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a -EBUILD emboss-6.6.0-r1.ebuild 1631 BLAKE2B 561dcc9b1dcf2cfe71e6c42e1770d8dfee2a25df7bb86da22d9fe934a118f974f2294f444c0047cd28794d9f94356a201a050c878c2185df20e0a7bea59d819c SHA512 27c4c445c27c3915fac4b35e997ae549c86669b8998c5086af7b533fc69366e118dbb4a8f833e79bd4b8f783af7e2424e398f4b898b002725c42780e24b66bf8 +DIST emboss-6.6.0-patches.tar.xz 5408 BLAKE2B ec1c55c90a64b1c27645804411b44e413ae881b1637ad2b8dfcff172e15b841cc3d2807039761f8307b0b5a29ab5b1a2c840e189f326091aa9ce25317ec9cda6 SHA512 942681df428f6254c1711902f667c6e8c71babf3e9b0c73b8b7d2fbfa5e8856ce5817560280948e588f6037011ad7055a3af5b88a58fc2b14349869927c889eb +EBUILD emboss-6.6.0-r1.ebuild 1827 BLAKE2B 4e8b0902b12d390abadbf5c9a9e2824a94bc5513aadb87959eb2faf245ad75246ee3080f75e2ebfb34792471e65350a3cee2a7f08837402b43d7e5608eb181d7 SHA512 e5297ce7678262a91c8749217f094a944b87eb157893542fe89fa6ffb770726959dfe8fd1a1f84aa349432a636419cf2cba6950e83bcc1a6c0156c97144b075e MISC metadata.xml 1096 BLAKE2B 704b6e7e0e9cb07a4cb184813ede8d7410d6612b2c8626838383a383dbd44f85b7f1dbcc988634f22d06ad76fbac927b4fd8a8836191be702c4f99a26343c6ac SHA512 4964b7e46d9fc16fcc44aaf83d0bb21a5ae860300764ca50e25f51ee0affc55fd863027747eb8e0eeca3578eefecbe23cba5ce68d518960e1721047cbefa9a3d diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild index 1c74ded5e22f..766dd6a61b0c 100644 --- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild +++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild @@ -8,7 +8,9 @@ EBO_EAUTORECONF=1 inherit emboss-r2 readme.gentoo-r1 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz" +SRC_URI=" + ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${P}-patches.tar.xz" S="${WORKDIR}/${P^^}" LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" @@ -29,10 +31,12 @@ PDEPEND=" )" PATCHES=( - "${FILESDIR}"/${P}_fix-build-system.patch - "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch - "${FILESDIR}"/${P}_plplot-declarations.patch - "${FILESDIR}"/${P}_qa-implicit-declarations.patch + "${WORKDIR}"/patches/${P}-fix-build-system.patch + "${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch + "${WORKDIR}"/patches/${P}-plplot-declarations.patch + "${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch + "${WORKDIR}"/patches/${P}-C99-bool.patch + "${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch ) src_install() { diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch deleted file mode 100644 index 7704873e9d26..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- EMBOSS-6.6.0/emboss/embossversion.c -+++ EMBOSS-6.6.0/emboss/embossversion.c -@@ -415,7 +415,7 @@ - ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); - #endif - #ifdef _FORTIFY_SOURCE -- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); -+ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); - #endif - ajFmtPrintF(outfile, "\n"); - ajFmtPrintF(outfile, "Sizes (bytes):\n"); diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch deleted file mode 100644 index 266bddd95a37..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ /dev/null @@ -1,411 +0,0 @@ - Makefile.am | 9 +++--- - ajax/Makefile.am | 4 +-- - ajax/acd/Makefile.am | 8 +++-- - ajax/ajaxdb/Makefile.am | 6 ++-- - ajax/core/Makefile.am | 6 ++-- - ajax/core/ajreg.h | 7 ++-- - ajax/ensembl/Makefile.am | 6 ++-- - ajax/graphics/Makefile.am | 8 +++-- - configure.ac | 82 ++++++++++++++++++++++++++--------------------- - emboss/Makefile.am | 13 +++++--- - jemboss/lib/Makefile.am | 2 +- - m4/idxdbs.m4 | 17 +++------- - nucleus/Makefile.am | 8 +++-- - 13 files changed, 100 insertions(+), 76 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index 177dec5..18dd99a 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -12,8 +12,11 @@ LICENSE \ - ONEWS \ - PROBLEMS - --SUBDIRS = \ --plplot \ -+SUBDIRS = -+if !ESYSTEMLIBS -+SUBDIRS += plplot -+endif -+SUBDIRS += \ - ajax \ - nucleus \ - emboss \ -@@ -33,5 +36,3 @@ dist-hook: - tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) - tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) - --install-exec-hook: -- $(bindir)/embossupdate -diff --git a/ajax/Makefile.am b/ajax/Makefile.am -index f27472c..de34e17 100644 ---- a/ajax/Makefile.am -+++ b/ajax/Makefile.am -@@ -1,7 +1,7 @@ - ## Process this file with automake to produce Makefile.in - --SUBDIRS = pcre -+SUBDIRS = - if !ESYSTEMLIBS --SUBDIRS += expat zlib -+SUBDIRS += pcre expat zlib - endif - SUBDIRS += core graphics ensembl ajaxdb acd -diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am -index 9f0f700..3295a1d 100644 ---- a/ajax/acd/Makefile.am -+++ b/ajax/acd/Makefile.am -@@ -3,16 +3,20 @@ - lib_LTLIBRARIES = libacd.la - - libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la - - libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics --libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - if !ESYSTEMLIBS -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libacd_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libacd_la_LDFLAGS = -version-info 6:5:0 -diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am -index c2b0c00..9de14fe 100644 ---- a/ajax/ajaxdb/Makefile.am -+++ b/ajax/ajaxdb/Makefile.am -@@ -3,14 +3,16 @@ - lib_LTLIBRARIES = libajaxdb.la - - libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la - - libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl --libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) - libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) - -diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am -index 2906837..3189c34 100644 ---- a/ajax/core/Makefile.am -+++ b/ajax/core/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libajax.la - - libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) - --libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajax_la_CPPFLAGS = - if !ESYSTEMLIBS -+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) - libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) - libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) -diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h -index 1623c82..5d928cf 100644 ---- a/ajax/core/ajreg.h -+++ b/ajax/core/ajreg.h -@@ -39,9 +39,8 @@ - #include "ajdefine.h" - #include "ajstr.h" - --#include "pcre_config.h" --#include "pcre_internal.h" --#include "pcreposix.h" -+#include -+#include - - AJ_BEGIN_DECLS - -@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS - - typedef struct AjSRegexp - { -- real_pcre *pcre; -+ struct real_pcre *pcre; - pcre_extra *extra; - int *ovector; - const char* orig; -diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am -index 0d1250b..5484c02 100644 ---- a/ajax/ensembl/Makefile.am -+++ b/ajax/ensembl/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libensembl.la - - libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libensembl_la_LIBADD = ../core/libajax.la - --libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libensembl_la_LDFLAGS = -version-info 6:5:0 -diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am -index a4f202b..1114c2c 100644 ---- a/ajax/graphics/Makefile.am -+++ b/ajax/graphics/Makefile.am -@@ -3,12 +3,16 @@ - lib_LTLIBRARIES = libajaxg.la - - libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) - --libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat --endif - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libajaxg_la_LDFLAGS = -version-info 6:5:0 -diff --git a/configure.ac b/configure.ac -index a7bd9c6..9ba3121 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -629,32 +629,6 @@ AS_CASE([${host_os}], - - - -- --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- - dnl Define where the EMBOSS package is located - AC_SUBST([AJAX_FIXED_ROOT]) - AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL - - - --dnl "Export" these variables for PCRE - --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) - - - -@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], - - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PCRE], [libpcre]) -+ PKG_CHECK_MODULES([EXPAT], [expat]) -+ PKG_CHECK_MODULES([ZLIB], [zlib]) -+ PKG_CHECK_MODULES([PLPLOT], [plplotd], -+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] -+ ) -+], -+[ -+dnl using bundled libraries -+ dnl PCRE library definitions - see the MAJOR and MINOR values -+ dnl to see which version's configure.ac these lines come from - -+ dnl Provide the current PCRE version information. Do not use numbers -+ dnl with leading zeros for the minor version, as they end up in a C -+ dnl macro, and may be treated as octal constants. Stick to single -+ dnl digits for minor numbers less than 10. There are unlikely to be -+ dnl that many releases anyway. -+ -+ PCRE_MAJOR="7" -+ PCRE_MINOR="9" -+ PCRE_DATE="11-Apr-2009" -+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -+ -+ dnl Default values for miscellaneous macros -+ -+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -+ -+ dnl Provide versioning information for libtool shared libraries that -+ dnl are built by default on Unix systems. -+ -+ PCRE_LIB_VERSION="0:1:0" -+ PCRE_POSIXLIB_VERSION="0:0:0" -+ -+ dnl "Export" these variables for PCRE -+ AC_SUBST([HAVE_MEMMOVE]) -+ AC_SUBST([HAVE_STRERROR]) -+ AC_SUBST([PCRE_MAJOR]) -+ AC_SUBST([PCRE_MINOR]) -+ AC_SUBST([PCRE_DATE]) -+ AC_SUBST([PCRE_VERSION]) -+ AC_SUBST([PCRE_LIB_VERSION]) -+ AC_SUBST([PCRE_POSIXLIB_VERSION]) -+ AC_SUBST([POSIX_MALLOC_THRESHOLD]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss/Makefile.am b/emboss/Makefile.am -index 89ada78..f987d40 100644 ---- a/emboss/Makefile.am -+++ b/emboss/Makefile.am -@@ -28,15 +28,18 @@ endif - - AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb -+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -+if !ESYSTEMLIBS - AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre --if !ESYSTEMLIBS - AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat - AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif --AM_CPPFLAGS += -I$(top_srcdir)/nucleus - AM_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+AM_CFLAGS += $(PLPLOT_CFLAGS) -+endif -+AM_CPPFLAGS += -I$(top_srcdir)/nucleus - AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) - AM_CPPFLAGS += $(JAVA_CPPFLAGS) - -@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la - if !ESYSTEMLIBS - LDADD += ../ajax/zlib/libezlib.la - LDADD += ../ajax/expat/libeexpat.la --endif - LDADD += ../ajax/pcre/libepcre.la - LDADD += ../plplot/libeplplot.la -+else -+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) -+endif - LDADD += $(XLIB) - - #if PURIFY -diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am -index 5f7e21e..8b45ce2 100644 ---- a/jemboss/lib/Makefile.am -+++ b/jemboss/lib/Makefile.am -@@ -12,7 +12,7 @@ mail.jar \ - jalviewApplet.jar \ - jemboss.jar - --jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java -+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java - if JAVA_BUILD - $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; - endif -diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 -index 0ca7ea9..9b54f2a 100644 ---- a/m4/idxdbs.m4 -+++ b/m4/idxdbs.m4 -@@ -1,17 +1,8 @@ - AC_DEFUN([CHECK_IDXDBS], - [ --AC_MSG_CHECKING(for EMBOSS pre-indexed databases) -+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) - -- --if test -f ./emboss/index/edam.xac; then --AC_MSG_RESULT(yes) --else --AC_MSG_RESULT(no) --echo "" --echo "Pre-indexed edam, taxon + drcat databases not found." --echo "Please download them from within this directory using:" --echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." --echo "and then repeat the configure step." --exit 1 --fi -+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], -+ [], -+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) - ]) -diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am -index 37b8543..5819c89 100644 ---- a/nucleus/Makefile.am -+++ b/nucleus/Makefile.am -@@ -3,6 +3,7 @@ - lib_LTLIBRARIES = libnucleus.la - - libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la - - if ISSHARED - if ISAIXIA64 -@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm - endif - endif - --libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot --libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib -+else -+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) - endif - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch deleted file mode 100644 index 15f5f967a07d..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.c -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c -@@ -49,7 +49,7 @@ - - #define GRAPH_DEBUG 1 - --#include "plplotP.h" -+#include - - - static void GraphArray(ajuint numofpoints, -@@ -964,10 +964,10 @@ - if(!thys->ready) - { - #if GRAPH_DEBUG -- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); -+ ajDebug("=g= plsfnam ('%S')\n", txt); - #endif - -- plxsfnam(ajStrGetPtr(txt), ext); -+ plsfnam(ajStrGetPtr(txt)); - ajStrAssignS(&graphBasename, txt); - ajStrAssignC(&graphExtension, ext); - if(ajStrGetCharFirst(graphExtension) == '.') -@@ -1213,10 +1213,10 @@ - void ajGraphicsSetPenwidth(float penwidth) - { - #if GRAPH_DEBUG -- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); -+ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); - #endif - -- plwid((PLINT)penwidth); -+ c_plwidth((PLINT)penwidth); - - return; - } -@@ -1538,10 +1538,10 @@ - static void GraphSetPen(ajint colour) - { - #if GRAPH_DEBUG -- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); -+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); - #endif - -- plcol((PLINT)colour); -+ plcol0((PLINT)colour); - - return; - } ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.h -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h -@@ -32,7 +32,7 @@ - /* ========================================================================= */ - - #include "ajdefine.h" --#include "plplot.h" -+#include - #include "ajgraphstruct.h" - #include "ajdefine.h" - #include "ajstr.h" diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch deleted file mode 100644 index eff10b2e6700..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch +++ /dev/null @@ -1,74 +0,0 @@ ---- EMBOSS-6.6.0/ajax/core/ajfeatread.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c -@@ -45,6 +45,7 @@ - - #include - #include -+#include - #include - - #ifdef WIN32 ---- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -@@ -43,7 +43,7 @@ - - #include - #include -- -+#include - - static AjPRegexp featoutRegUfoFmt = NULL; - static AjPRegexp featoutRegUfoFile = NULL; ---- EMBOSS-6.6.0/ajax/core/ajpdbio.c -+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c -@@ -37,7 +37,7 @@ - - #include - #include -- -+#include - - - ---- EMBOSS-6.6.0/ajax/core/ajreg.c -+++ EMBOSS-6.6.0/ajax/core/ajreg.c -@@ -32,6 +32,7 @@ - #include "ajlib.h" - - #include "ajreg.h" -+#include - - - ---- EMBOSS-6.6.0/ajax/core/ajseqtype.c -+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c -@@ -32,7 +32,7 @@ - #include "ajfeat.h" - #include "ajfile.h" - #include "ajreg.h" -- -+#include - - - ---- EMBOSS-6.6.0/nucleus/embindex.c -+++ EMBOSS-6.6.0/nucleus/embindex.c -@@ -35,6 +35,7 @@ - #include "ajnam.h" - - #include -+#include - - #define BTENTRYFILE ".ent" - #define KWLIMIT 12 ---- EMBOSS-6.6.0/nucleus/embword.c -+++ EMBOSS-6.6.0/nucleus/embword.c -@@ -36,7 +36,7 @@ - #include "ajutil.h" - - #include -- -+#include - - - -- cgit v1.2.3