commit: fa85d5355b3c7d3f6d25127e1b6f4ea7450a5a88 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Jan 1 12:42:51 2018 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Jan 1 12:42:51 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fa85d535
sci-biology/arb: Remove old Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/arb/Manifest | 7 --- sci-biology/arb/arb-5.1-r1.ebuild | 77 --------------------------- sci-biology/arb/arb-5.2.ebuild | 79 ---------------------------- sci-biology/arb/arb-5.3.ebuild | 77 --------------------------- sci-biology/arb/files/5.1-bfr-overflow.patch | 16 ------ sci-biology/arb/files/5.1-libs.patch | 16 ------ sci-biology/arb/files/5.2-libpng15.patch | 45 ---------------- sci-biology/arb/files/arb-5.2-gcc-47.patch | 15 ------ 8 files changed, 332 deletions(-) diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest index 60bfb783165..4f19d30ed17 100644 --- a/sci-biology/arb/Manifest +++ b/sci-biology/arb/Manifest @@ -1,8 +1 @@ -DIST arb-5.1-glibc2.10.patch.bz2 24659 BLAKE2B 856b4735c98f13b21af537486f27ae89cca724590f7f4d7975dc7df05d3e3388a29198f6b9bb14b2ef885f5442d6687d6fbcdb44c076656b8e2ff521c633f940 SHA512 a490066efc5001e22bfeab8ce3e05690f5024217261b7b71c5a31116d18611a93f5b15aa7d57fca40e2b5e17e64b695873ccb810bd649b2b109c9b710d3ddfe1 -DIST arb-5.1-linker.patch.bz2 4406 BLAKE2B 3214f875c7d58e9a60032397f34a38ec13fc1672cecca475223fe8b79c684d4839e3e7dcf7c1df8290f00912b6268493bf89d77b744c923b3a9769bb466bef15 SHA512 44518d500be457d16e7f6cd5f0863d2dc48cc8a1c8abcbaea79eefec5cd063258aea78d03e9601cd0bdea3c7e57949373d7a909eeed98bf48a6d98576f298e58 -DIST arb-5.1.tgz 9727285 BLAKE2B 97660214b1dc513a946256cfdcbbefff282bb125e81e05a92005bd62b4ec00a478fb6639c6f5b0b3893e1c49d8eb9f13d04ec36271daec41c41b9093fefea09a SHA512 236f7c40217146cf5b43d15c7252901a09f2081c1da6db1b90d7720d313e21a2808b31879d700bf894b3c576952c43be751fd0027af8a58d953403028589dd8c -DIST arb-5.2-linker.patch.bz2 4441 BLAKE2B c2554cf4e24ab9257dfac06482f05a42e89ad06ecf1b069d80df16d512ce675a29f7c3dbe0bca6b0f3add910617cc5853462aa5593cb9ccb2fb2656cdd5183c1 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 -DIST arb-5.2.tgz 9729004 BLAKE2B 2ae85529c9c7afdbc0debc0317e0ab3772f881b606f849b6cb60872e2e123b612399dc4dcfa07c5e886703478140515fa31e9b69b37383a12d8526ecb771f77b SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 -DIST arb-5.3-linker.patch.xz 3604 BLAKE2B 0327a94ee4daaca9cc4aa41601ae52b8616d26fd0ede19b36cb2ea72135bc9609d21db74b9588cc79e08242d3e32bb3398d78663c90dc4e3c248877953249789 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 -DIST arb-5.3.tgz 9543106 BLAKE2B e67859accad1f5aeae3fe3a85530543beb1141e1fe340760e55b2bcef84f1f5cd18fe82ff75beafbf49b1945def0436d862487a630192345568931a335454210 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 DIST arb-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4 diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild deleted file mode 100644 index f52beded359..00000000000 --- a/sci-biology/arb/arb-5.1-r1.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=2 - -inherit eutils toolchain-funcs - -DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" -HOMEPAGE="http://www.arb-home.de/"; -SRC_URI=" - http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz - mirror://gentoo/${P}-glibc2.10.patch.bz2 - https://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"; - -LICENSE="arb" -SLOT="0" -IUSE="+opengl" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - app-text/sablotron - media-libs/libpng - media-libs/tiff - www-client/lynx - x11-libs/libXaw - x11-libs/libXpm - x11-libs/motif:0 - opengl? ( - media-libs/glew - media-libs/freeglut - || ( - media-libs/mesa[motif] - ( media-libs/mesa x11-libs/libGLw ) ) )" -RDEPEND="${DEPEND} - sci-visualization/gnuplot" -# Recommended: libmotif3 gv xfig xterm treetool java - -src_unpack() { - unpack ${A} - mv arbsrc* ${P} -} - -src_prepare() { - epatch \ - "${WORKDIR}"/${P}-glibc2.10.patch\ - "${WORKDIR}"/${P}-linker.patch \ - "${FILESDIR}"/${PV}-libs.patch \ - "${FILESDIR}"/${PV}-bfr-overflow.patch - sed -i \ - -e 's/all: checks/all:/' \ - -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ - -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ - -e 's/--export-dynamic/-Wl,--export-dynamic/g' \ - "${S}/Makefile" || die - cp config.makefile.template config.makefile - sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die - use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile - use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile - emake ARBHOME="${S}" links || die -} - -src_compile() { - emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die - use amd64 && mv arb.tgz arb.64.gentoo.tgz - use x86 && mv arb.tgz arb.32.gentoo.tgz - ln -s arb.*.tgz arb.tgz || die -} - -src_install() { - ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die - cat <<- EOF > "${S}/99${PN}" - ARBHOME=/opt/arb - PATH=/opt/arb/bin - LD_LIBRARY_PATH=/opt/arb/lib - EOF - doenvd "${S}/99${PN}" || die -} diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild deleted file mode 100644 index a7388bf9b81..00000000000 --- a/sci-biology/arb/arb-5.2.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils toolchain-funcs - -DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" -HOMEPAGE="http://www.arb-home.de/"; -SRC_URI=" - http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz - https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"; - -SLOT="0" -LICENSE="arb" -IUSE="+opengl" -KEYWORDS="~amd64 ~x86" - -CDEPEND="app-text/sablotron - media-libs/libpng - media-libs/tiff - www-client/lynx - x11-libs/libXaw - x11-libs/libXpm - x11-libs/motif:0 - opengl? ( - media-libs/glew - media-libs/freeglut - || ( - media-libs/mesa[motif] - ( media-libs/mesa x11-libs/libGLw ) ) )" -DEPEND="${CDEPEND} - sys-process/time" -RDEPEND="${CDEPEND} - sci-visualization/gnuplot" -# Recommended: libmotif3 gv xfig xterm treetool java - -src_unpack() { - unpack ${A} - mv arbsrc* ${P} -} - -src_prepare() { - epatch \ - "${WORKDIR}"/${P}-linker.patch \ - "${FILESDIR}"/5.1-libs.patch \ - "${FILESDIR}"/5.1-bfr-overflow.patch \ - "${FILESDIR}"/${PV}-libpng15.patch \ - "${FILESDIR}"/${P}-gcc-47.patch - sed \ - -e 's/all: checks/all:/' \ - -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ - -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ - -e 's:-O4::g' \ - -e 's:-pipe::g' \ - -i "${S}/Makefile" || die - cp config.makefile.template config.makefile - sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die - use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile - use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile - emake ARBHOME="${S}" links -} - -src_compile() { - emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile - use amd64 && mv arb.tgz arb.64.gentoo.tgz - use x86 && mv arb.tgz arb.32.gentoo.tgz - ln -s arb.*.tgz arb.tgz || die -} - -src_install() { - ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die - cat <<- EOF > "${S}/99${PN}" - ARBHOME=/opt/arb - PATH=/opt/arb/bin - LD_LIBRARY_PATH=/opt/arb/lib - EOF - doenvd "${S}/99${PN}" -} diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild deleted file mode 100644 index 135bec2695c..00000000000 --- a/sci-biology/arb/arb-5.3.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils toolchain-funcs - -DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" -HOMEPAGE="http://www.arb-home.de/"; -SRC_URI=" - http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz - https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"; - -SLOT="0" -LICENSE="arb" -IUSE="+opengl" -KEYWORDS="~amd64 ~x86" - -CDEPEND="app-text/sablotron - media-libs/libpng - media-libs/tiff - www-client/lynx - x11-libs/libXaw - x11-libs/libXpm - x11-libs/motif:0 - opengl? ( - media-libs/glew - media-libs/freeglut - || ( - media-libs/mesa[motif] - ( media-libs/mesa x11-libs/libGLw ) ) )" -DEPEND="${CDEPEND} - sys-process/time" -RDEPEND="${CDEPEND} - sci-visualization/gnuplot" -# Recommended: libmotif3 gv xfig xterm treetool java - -src_unpack() { - unpack ${A} - mv arbsrc* ${P} -} - -src_prepare() { - epatch \ - "${WORKDIR}"/${P}-linker.patch \ - "${FILESDIR}"/5.1-libs.patch \ - "${FILESDIR}"/5.1-bfr-overflow.patch \ - "${FILESDIR}"/5.2-libpng15.patch \ - "${FILESDIR}"/${PN}-5.2-gcc-47.patch - sed \ - -e 's/all: checks/all:/' \ - -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ - -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ - -i "${S}/Makefile" || die - cp config.makefile.template config.makefile - sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die - use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile - use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile - emake ARBHOME="${S}" links -} - -src_compile() { - emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile - use amd64 && mv arb.tgz arb.64.gentoo.tgz - use x86 && mv arb.tgz arb.32.gentoo.tgz - ln -s arb.*.tgz arb.tgz || die -} - -src_install() { - ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die - cat <<- EOF > "${S}/99${PN}" - ARBHOME=/opt/arb - PATH=/opt/arb/bin - LD_LIBRARY_PATH=/opt/arb/lib - EOF - doenvd "${S}/99${PN}" -} diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch deleted file mode 100644 index 21d21f5ac17..00000000000 --- a/sci-biology/arb/files/5.1-bfr-overflow.patch +++ /dev/null @@ -1,16 +0,0 @@ - ARB_GDE/GDE_HGLfile.cxx | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx -index e353a89..f69635a 100644 ---- a/ARB_GDE/GDE_HGLfile.cxx -+++ b/ARB_GDE/GDE_HGLfile.cxx -@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type) - if(this_elem->id[0] == '\0') - strncpy(this_elem->id,uniqueID(),79); - if(this_elem->short_name[0] == '\0') -- strncpy(this_elem->short_name,this_elem->id,79); -+ strncpy(this_elem->short_name,this_elem->id,31); - if(this_elem->seqlen == 0) - this_elem->protect= - PROT_BASE_CHANGES+ diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch deleted file mode 100644 index bf0bacad328..00000000000 --- a/sci-biology/arb/files/5.1-libs.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl -index b653a66..b346c96 100644 ---- a/SOURCE_TOOLS/provide_libs.pl -+++ b/SOURCE_TOOLS/provide_libs.pl -@@ -118,11 +118,6 @@ sub provide_libs($$$) { - foreach my $lib (keys %needed_by) { - update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir); - } -- if ($opengl==1) { -- foreach my $lib (keys %needed_by_opengl) { -- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir); -- } -- } - } - - sub main() { diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch deleted file mode 100644 index 3d750e76efe..00000000000 --- a/sci-biology/arb/files/5.2-libpng15.patch +++ /dev/null @@ -1,45 +0,0 @@ -Fix building with libpng-1.5 - -https://bugs.gentoo.org/show_bug.cgi?id=378353 - -Patch written by Samuli Suominen <[email protected]> ---- a/GL/glpng/glpng.c -+++ b/GL/glpng/glpng.c -@@ -285,7 +285,7 @@ - endinfo = png_create_info_struct(png); - - // DH: added following lines -- if (setjmp(png->jmpbuf)) -+ if (setjmp(png_jmpbuf(png))) - { - png_destroy_read_struct(&png, &info, &endinfo); - return 0; -@@ -390,7 +390,7 @@ - endinfo = png_create_info_struct(png); - - // DH: added following lines -- if (setjmp(png->jmpbuf)) -+ if (setjmp(png_jmpbuf(png))) - { - png_destroy_read_struct(&png, &info, &endinfo); - return 0; -@@ -569,7 +569,7 @@ - #define ALPHA *q - - switch (trans) { -- case PNG_CALLBACK: -+ case PNG_CALLBACKT: - FORSTART - ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b); - FOREND ---- a/GL/glpng/glpng.h -+++ b/GL/glpng/glpng.h -@@ -57,7 +57,7 @@ - #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS - - /* Transparency parameters */ --#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */ -+#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */ - #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */ - #define PNG_SOLID -1 /* No transparency */ - #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */ diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch deleted file mode 100644 index 186e78e450b..00000000000 --- a/sci-biology/arb/files/arb-5.2-gcc-47.patch +++ /dev/null @@ -1,15 +0,0 @@ - AWTI/AWTI_import.cxx | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx -index 8e730ac..e3f9ff4 100644 ---- a/AWTI/AWTI_import.cxx -+++ b/AWTI/AWTI_import.cxx -@@ -12,6 +12,7 @@ - #include <GEN.hxx> - - #include <climits> -+#include <unistd.h> - - using namespace std; -
