diff options
Diffstat (limited to 'sci-chemistry')
33 files changed, 76 insertions, 894 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex dbbd5c59e90e..c4dade297655 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest deleted file mode 100644 index de2fa35a0b3d..000000000000 --- a/sci-chemistry/aqua/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX aqua-3.2-flags.patch 4211 BLAKE2B 032048ea0f08aa798758489beda88aa0f07635e7ee965d25791b73a2995224920392c7eaf52b0da97d4e0df70df9901d5dd915c2a0adc499e6e17160e2fac467 SHA512 059cea5403fb4cb01b0fcd4d2a2fe4b4aea725e9362a6188ccd3756ced35e324cda5efb21d3ad2a95a842e9d83f8e728a16b36e4b6a479ae32da8816d7eafdfc -DIST aqua-3.2-nmr_manual.tar.gz 632031 BLAKE2B 1f595a111af4b5e91fc059b5af590a6c37a44654fcae42e6003b40cf7fdf542cb772d3ef25bf2475455ce8638cd0aebcbbc8c66bb57688ce919af2eac9b535cb SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f -DIST aqua3.2.tar.gz 688408 BLAKE2B 898e0e3bbc4ff7b6ce8a8128ce6ffef45db607c74e2d78a70cefc26818d39049e4d18159b65250a3651112f64318ccce838037e563d3a985be7ef369d89b594e SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a -EBUILD aqua-3.2-r3.ebuild 2087 BLAKE2B 053412cfb8802a1fd07e2ab53e19d8cca8f422063bd0d64723e2152b4d2fce4fc4597db2fd906b08b899937fac27c390abf73e1638f0a77f356e3bf86dea7d7f SHA512 1d5e6cdefb415613ade4170837b0092772a2c76bbb29b4c10e6ef75044f380c724371509fc5ec50144828bc6dcbd04b282135a0147561b424267331ad79b802a -MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049 diff --git a/sci-chemistry/aqua/aqua-3.2-r3.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild deleted file mode 100644 index 78d987ec1460..000000000000 --- a/sci-chemistry/aqua/aqua-3.2-r3.ebuild +++ /dev/null @@ -1,97 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit fortran-2 toolchain-funcs - -DESCRIPTION="Program suite in this distribution calculates restraint violations" -HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" -SRC_URI=" - ${PN}${PV}.tar.gz - doc? ( ${P}-nmr_manual.tar.gz )" - -SLOT="0" -LICENSE="procheck" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" - -RDEPEND="sci-chemistry/procheck" -DEPEND="app-shells/tcsh" - -RESTRICT="fetch" - -S="${WORKDIR}"/${PN}${PV} - -PATCHES=( - "${FILESDIR}"/${P}-flags.patch -) - -pkg_nofetch() { - elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" - elog "And follow the instructions for downloading the following into your DISTDIR" - elog "directory:" - elog " ${PN}${PV}.tar.gz" - if use doc; then - elog " nmr_manual.tar.gz -> ${P}-nmr_manual.tar.gz" - fi -} - -src_prepare() { - sed \ - -e 's:nawk:gawk:g' \ - -e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \ - -e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \ - -i $(find . -type f) || die - default -} - -src_compile() { - cd src || die - emake \ - MYROOT="${WORKDIR}" \ - CC="$(tc-getCC)" \ - FC="$(tc-getFC)" \ - CFLAGS="${CFLAGS} -I../sub/lib" \ - FFLAGS="${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - exth - emake \ - MYROOT="${WORKDIR}" \ - CC="$(tc-getCC)" \ - FC="$(tc-getFC)" \ - CFLAGS="${CFLAGS} -I../sub/lib" \ - FFLAGS="${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - rm -f scripts/conv* || die - dobin bin/* scripts/* - dosym AquaWhat /usr/bin/qwhat - dosym AquaHow /usr/bin/qhow - dosym AquaPseudo /usr/bin/qpseudo - dosym AquaDist /usr/bin/qdist - dosym AquaCalc /usr/bin/qcalc - dosym AquaAssign /usr/bin/qassign - dosym AquaRedun /usr/bin/qredun - dosym AquaCompl /usr/bin/qcompl - - dodoc HISTORY HOW_TO_USE NEW README doc/* - dohtml html/* - - insinto /usr/share/${PN} - doins data/* - if use examples; then - doins -r exmpls - fi - - if use doc; then - dohtml -r manual - fi - - cat >> "${T}"/34aqua <<- EOF - AQUADATADIR="${EPREFIX}/usr/share/${PN}" - EOF - doenvd "${T}"/34aqua -} diff --git a/sci-chemistry/aqua/files/aqua-3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch deleted file mode 100644 index a60841b8ce08..000000000000 --- a/sci-chemistry/aqua/files/aqua-3.2-flags.patch +++ /dev/null @@ -1,84 +0,0 @@ -diff --git a/src/makefile b/src/makefile -index 3113471..dd7a320 100644 ---- a/src/makefile -+++ b/src/makefile -@@ -176,47 +176,46 @@ nrutil.h: - # Executable files - - $(BIN)/AquaWhat: AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) - - $(BIN)/AquaHow: AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) - - $(BIN)/AquaPseudo: AquaPseudo.o $(OBJECTS) $(R_OBJECTS) -- $(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) - - $(BIN)/AquaDist: AquaDist.o $(OBJECTS) -- $(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm - - $(BIN)/AquaCalc: AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm - - $(BIN)/AquaAssign: AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) - - $(BIN)/AquaCompl: AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm - - $(BIN)/AquaRedun: AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -- $(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) - - $(BIN)/testnew: testnew.o $(OBJECTS) -- $(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS) - - $(BIN)/getproj: getproj.c -- $(CC) -o $(BIN)/getproj -O getproj.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c - - $(BIN)/AquaPlot: AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o -- $(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o - - $(BIN)/Qext: Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o -- $(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o - - $(BIN)/StarTest: StarTest.o -- $(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS) - - exth: exth.f -- f77 -o exth -O2 exth.f -- strip exth -+ $(FC) $(FFLAGS) $(LDFLAGS) -o exth -O2 exth.f - - - # Object files -@@ -269,7 +268,7 @@ AquaCommon.o: AquaCommon.c AquaCommon.h nrutil.h \ - $(CC) -c AquaCommon.c $(CFLAGS) - - nrutil.o: nrutil.c nrutil.h -- $(CC) -c nrutil.c -DANSI -+ $(CC) $(CFLAGS) -c nrutil.c -DANSI - - AquaFuncts.o: AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\ - AquaStrucset.h AquaFiles.h\ -@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o: $(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\ - cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS) - - cv_subs.o: cv_subs.f -- f77 -c cv_subs.f $(FFLAGS) -+ $(FC) -c cv_subs.f $(FFLAGS) - - Qext.o: Qext.c Qext.h\ - $(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS) diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml deleted file mode 100644 index d4ff1000a775..000000000000 --- a/sci-chemistry/aqua/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest index 6b275a888424..25d061c91462 100644 --- a/sci-chemistry/mopac7/Manifest +++ b/sci-chemistry/mopac7/Manifest @@ -2,5 +2,5 @@ AUX Makefile 387 BLAKE2B b0c4b3a009c8bf8c779953edf3e233434656033a661cb307079eebc DIST dcart.f 11044 BLAKE2B 7414804ecfab9a7cbddee664b85e6e2e8c1d8fe1e1f73d480dd1a387c5e349d26ec4ae1a37f27e38b7c051fcce2c1bdf77de12ec628298fd3edf79040a8a0c5a SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80 DIST gmxmop.f 38956 BLAKE2B e411feca5104e91ae8fd2008de61d18cc214beb3b2a7aa09a80269fb935e27ba1b1cb89fa30eedbfc4f6c4734c22d932e57d5905c175ae9f56c4affee7b0ca04 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194 DIST mopac7-1.15.tar.gz 764547 BLAKE2B 6e037862007221955d0ad65f3c002a3d2e461950a2bc0efac9d195cf1d9d856842d02bc380ce236c3d48f863a144875950f5c86f8f3ac936b8b098472f7f7a0d SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e -EBUILD mopac7-1.15-r1.ebuild 1855 BLAKE2B e3ecda4d53b2d1f8161cf5fbac788149302e1fbaf972fdba2e372c2ad6535e2c55055f1486788c5e2e8b0027fff6d9532ebd5566c032390a507f0b5b072b2d75 SHA512 3dc54baa3559c0bc297ba4b50337255774a4a74ba3d4a2a38fe213325e13aa13f288b2d783ec082ce042979fe3f57d914d570a17e5d6858833ba2f7a66af145f +EBUILD mopac7-1.15-r1.ebuild 1979 BLAKE2B 9ed2f685e1b787f1eece439ca75efe489601651712aa6dbab8fff05d78e0ce3d97a5116266568d985e2ca67749e4bd39dd606f8f419141ce39ccadf39de9fe22 SHA512 add91d8a0b7da52ecebed3f611fb259110ab4872554ea2db94bb476625ef2c09ea83220f6e16f69303c6bba368bbd1681ec293f013cfce05a05b6a3271438d0a MISC metadata.xml 435 BLAKE2B 12efd7ecfe6c9b07411d62992a225848f3787b58a59765e373fdc98ce22c3b50763243ac70efa1d7a7ec3309bc519dd433d41b778fe8f18cdfbdae971e0ee82c SHA512 d624b1181bdd0d66062507e7793eb25d24c447fa9ffbe8ee1645c88b843e6822e80af087bf6073ac191947074491159331f2021b884f8b7cd2237cf3e013ebb4 diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild index f785669fe7f4..c536575112e8 100644 --- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild +++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -39,6 +39,12 @@ src_prepare() { } src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/927389 + # + # Unmaintained fortran code, no bug report. + filter-lto + econf --disable-static } diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest deleted file mode 100644 index 4d348875c0d2..000000000000 --- a/sci-chemistry/namd/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX namd-2.10-gentoo.patch 4637 BLAKE2B 0439e424f3d2a73378c68052f9d9dd69dc9590b9f83fa4062d4abc156b3b682f0e8a2cffd8a1e1f751f8dfd71d067c0234ba56946773ca9139e73c57e775c631 SHA512 35afda71ad7567d1b2c4c1f4073792d5977edc997ba7a43cf71c8ed32308062edc5cb4923202d599d59ade2f98602a0fac21138ba205a3bf6b681c86a61411f8 -AUX namd-2.7-iml-dec.patch 520 BLAKE2B c16430d1161b9d7e3faf22257d84ff1090eccf906a296f91d4ec0731fa89d23334d5c39c7988f8ac6d5f5020d403d4491dadbe34b1e9800ada81ad18b2448b7d SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37 -DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 -EBUILD namd-2.10.ebuild 2644 BLAKE2B 6d91c9f7f90f2b304c18bb176e7fdfcfff98a077bf8d6ed720b24ee186b5dece164fde49cee6db3f3dff217a53bba76d6d1c00b45ca7633ab1d9fb2a0b53ef46 SHA512 816bc445d23cc15fcf7d17bacb11b7ae4566a7bf135a88f80b7587d9630db0650e0f8b54b828bbbe8454008b6967fc276fbfc347cda351ec4b9e370d08671e08 -MISC metadata.xml 377 BLAKE2B 727b1c499d11b56228aab0bb2c47c45f63c48a1406f52b5b3d3fe8d02b69d0113dbad00eca99bcff194fc164605b2b698bdd8581c20fb6401c54169265d73f6b SHA512 4dbe460b1b9a0a8112d7866a11a389a1e2847afa3404c57479bdf39e6b3600d403c5c1f70d76196cd1508770dcd8befcc73687969b6853ff1e5f25cf5d22fea7 diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch deleted file mode 100644 index ffef6dc3ad68..000000000000 --- a/sci-chemistry/namd/files/namd-2.10-gentoo.patch +++ /dev/null @@ -1,124 +0,0 @@ -diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw ---- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux-x86_64 -+FFTDIR=/usr - FFTINCL=-I$(FFTDIR)/include --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl ---- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 -@@ -1,9 +1,9 @@ - - #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 --TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded -+TCLDIR=/usr - TCLINCL=-I$(TCLDIR)/include - #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl --TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread -+#TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread - TCLFLAGS=-DNAMD_TCL - TCL=$(TCLINCL) $(TCLFLAGS) - -diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile ---- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 -@@ -389,10 +389,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/gentoo-libdir - CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast - #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB - #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -@@ -418,7 +418,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun -+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -434,7 +434,7 @@ - - namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) -- $(CHARMC) -verbose -ld++-option \ -+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ - '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ - "$(CHARM_MODULES)" -language charm++ \ - $(BUILDINFO).o \ -@@ -484,11 +484,8 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) -- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm -+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - - psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm -@@ -506,7 +503,7 @@ - $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm - - flipdcd: $(SRCDIR)/flipdcd.c -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ - echo "#!/bin/sh\necho unavailable on this platform" > $@; \ - chmod +x $@ - -@@ -516,7 +513,7 @@ - chmod +x $@ - - fixdcd: $(SRCDIR)/fixdcd.c -- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c - - dumpdcd: $(SRCDIR)/dumpdcd.c - $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c -@@ -711,9 +708,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 -- --WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) -+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -724,17 +719,9 @@ - for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ - /bin/rm -rf $$f; \ - done -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done - - winrelease: winall diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch deleted file mode 100644 index e5ee3bd6c818..000000000000 --- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c -index 94b71ba..01a2529 100644 ---- a/src/flipbinpdb.c -+++ b/src/flipbinpdb.c -@@ -9,6 +9,7 @@ - #include <sys/mman.h> - #include <fcntl.h> - #include <stdio.h> -+#include <stdlib.h> - - #ifndef MAP_FILE - #define MAP_FILE 0 -diff --git a/src/flipdcd.c b/src/flipdcd.c -index 8ec85b7..1c23433 100644 ---- a/src/flipdcd.c -+++ b/src/flipdcd.c -@@ -13,6 +13,7 @@ - #include <sys/mman.h> - #include <fcntl.h> - #include <stdio.h> -+#include <stdlib.h> - - #ifndef MAP_FILE - #define MAP_FILE 0 diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml deleted file mode 100644 index 11bbcb9bf2c8..000000000000 --- a/sci-chemistry/namd/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>nicolasbock@gentoo.org</email> - <name>Nicolas Bock</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild deleted file mode 100644 index 76a34c5a0a19..000000000000 --- a/sci-chemistry/namd/namd-2.10.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PN="NAMD" - -inherit multilib toolchain-funcs flag-o-matic - -DESCRIPTION="A powerful and highly parallelized molecular dynamics code" -HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" -SRC_URI="${MY_PN}_${PV}_Source.tar.gz" - -LICENSE="namd" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -RESTRICT="fetch" - -RDEPEND=" - >=sys-cluster/charm-6.5.1-r2 - sci-libs/fftw:3.0 - dev-lang/tcl:0=" - -DEPEND="${RDEPEND} - virtual/pkgconfig - app-shells/tcsh" - -NAMD_ARCH="Linux-x86_64-g++" - -NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" - -S="${WORKDIR}/${MY_PN}_${PV}_Source" - -PATCHES=( - # apply a few small fixes to make NAMD compile and - # link to the proper libraries - "${FILESDIR}"/namd-2.10-gentoo.patch - "${FILESDIR}"/namd-2.7-iml-dec.patch -) - -pkg_nofetch() { - echo - einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" - einfo "${NAMD_DOWNLOAD}" - einfo "after agreeing to the license and then move it to" - einfo "your DISTDIR directory." - einfo "Be sure to select the ${PV} version!" - echo -} - -src_prepare() { - CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) - - default - - sed \ - -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \ - -i Make.charm || die - - # Remove charm distribution. We don't need it. - rm -f charm-*.tar || die - - # proper compiler and cflags - sed \ - -e "s/g++.*/$(tc-getCXX)/" \ - -e "s/gcc.*/$(tc-getCC)/" \ - -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ - -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ - -i arch/${NAMD_ARCH}.arch || die - - sed \ - -e "s/gentoo-libdir/$(get_libdir)/g" \ - -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ - -i Makefile || die "Failed gentooizing Makefile." - sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die - sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die -} - -src_configure() { - # configure - ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die -} - -src_compile() { - # build namd - cd "${S}/${NAMD_ARCH}" || die - TCLLIB="$($(tc-getPKG_CONFIG) --libs tcl) -ldl -pthread" \ - emake -} - -src_install() { - dodoc announce.txt license.txt notes.txt - cd "${S}/${NAMD_ARCH}" || die - - # the binaries - dobin ${PN}2 psfgen flipbinpdb flipdcd -} - -pkg_postinst() { - echo - einfo "For detailed instructions on how to run and configure" - einfo "NAMD please consults the extensive documentation at" - einfo "http://www.ks.uiuc.edu/Research/namd/" - einfo "and the NAMD tutorials available at" - einfo "http://www.ks.uiuc.edu/Training/Tutorials/" - einfo "Have fun :)" - echo -} diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index f11612320ce8..12ada1118c65 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -3,6 +3,6 @@ AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 -EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7464 BLAKE2B 3c3b12086a4b69c1ccfd92b5da672ff2ec4a1dc161832094d62b049977e0cb8d8717e5999f3138f857efb642a123a64fca804c5a109f69de939686fae9a08bd8 SHA512 0b516f2a8cb7194d2146397c3fc1ef375446d8dd6a29d862ed73e78455e41c0d9a86cdaee7de64cd2d4403dac34b0ec8fee4e68156df7562331d4577c82f411c -EBUILD openbabel-9999.ebuild 7314 BLAKE2B 4bb03f325ec2876317c4f13d481b2f7738989358bd7707f27f6f650e3e41a9afe758721b4c4929a664eb09f82fbb8da0ba9dba8331f687c36758547345ce2ef0 SHA512 37b58ea4747b79b6dcfc5e5cd69af8f1d37b2a6a1c8bf414116396549094db9e89133b70a944ab3b7668eb9d815c7e4ae9fcff9a877cea85a00911e44682eb0a +EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195 +EBUILD openbabel-9999.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195 MISC metadata.xml 921 BLAKE2B c0797440e50f813777c4858cc1ce893546d7785e57243318ec7d2c601c6ec2ecb7ec5ab3dbacce960c8b71196eef51ddce07802257fff0d4cba0293f940a773f SHA512 8ee8a50230f374904a9ddaaf7337caf018788ab25a1839dbf5a48b0e5c49ac4e285a1fa759900fa6d993bc220d3586a923ae21158687be971fc51a6c302f12ad diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild index bdfef2a675e8..fc4d6cab575e 100644 --- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild +++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) WX_GTK_VER=3.2-gtk3 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild index d533ec698acf..fc4d6cab575e 100644 --- a/sci-chemistry/openbabel/openbabel-9999.ebuild +++ b/sci-chemistry/openbabel/openbabel-9999.ebuild @@ -3,13 +3,13 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) WX_GTK_VER=3.2-gtk3 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils DESCRIPTION="Interconverts file formats used in molecular modeling" -HOMEPAGE="https://openbabel.org/" +HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/" if [[ "${PV}" == *9999* ]]; then inherit git-r3 @@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then else if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325 # Set to commit hash - OPENBABEL_COMMIT= + OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}" else @@ -25,7 +25,7 @@ else SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${PN}-${MY_P}" fi - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" fi SRC_URI="${SRC_URI} @@ -80,6 +80,10 @@ RDEPEND=" ) " +PATCHES=( + "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch +) + pkg_pretend() { [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp } diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest deleted file mode 100644 index 176af33f9d5a..000000000000 --- a/sci-chemistry/procheck/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX procheck-3.5.4-close.patch 1073 BLAKE2B 54e9857e3d3ee920becebfc50da34145384046be019a2fcd01d47afc4f9242a5311aac166dcde7dc79de584c2ea08bd8e766ae58310700bff45f6bb1a2829abf SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307 -AUX procheck-3.5.4-ldflags.patch 1649 BLAKE2B 64506db2dbe1eba43dfc07bca233d573646ac553862e8d6eecce7970362047cfd8fdcd18f7c83bb74a0476fde78222ea92e0c2a56b24fba2d71d9c97c563fbb1 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f -DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a -DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c -DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc -EBUILD procheck-3.5.4-r3.ebuild 1717 BLAKE2B 1919325faefdc9cad032d503166cdedc966f44c949bf1c2c34d3aa7b0132fdbb35a3a7e0f446a967166cbce66596143e114cea7b0c23aa9ca0c99acd9c29ec4a SHA512 04c58e977937275fd413ff217d97f7fa0dfacca2492c57b60d8f2d671565e640852c391e8c408618ed3e9da53f602f96c2863a009d8798011365a9b9f1fa93ec -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch deleted file mode 100644 index 16a0658e654d..000000000000 --- a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch +++ /dev/null @@ -1,35 +0,0 @@ -diff --git a/pplot.f b/pplot.f -index 7e06e68..c86b2b2 100644 ---- a/pplot.f -+++ b/pplot.f -@@ -4720,6 +4720,7 @@ C---- Initialise variables - SCORE(IDIST) = 0.0 - 50 CONTINUE - -+ REWIND(3) - C---- If the required residue is of a greater number than that required, - C read through the file until come to it - IF (IRESID.GT.INRES) THEN -diff --git a/ps.f b/ps.f -index b652a7d..858b8e5 100644 ---- a/ps.f -+++ b/ps.f -@@ -1705,12 +1705,14 @@ CVAX - CARRIAGECONTROL='LIST', - C---- If this is an existing file, then read through all its records until - C get to the end of file - IF (.NOT.NEWFIL) THEN -+ CLOSE(14) -+ OPEN(14, file=fname, status='old', position='append', err=900) - - C---- Loop through the file until reach the end -- 100 CONTINUE -- READ(14,110,END=500) IREC -- 110 FORMAT(A) -- GO TO 100 -+C 100 CONTINUE -+C READ(14,110,END=500) IREC -+C 110 FORMAT(A) -+C GO TO 100 - - C---- If this is a new file, then write the header records to it - ELSE
\ No newline at end of file diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch deleted file mode 100644 index 453aebe3211f..000000000000 --- a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch +++ /dev/null @@ -1,49 +0,0 @@ -diff --git a/Makefile b/Makefile -index c5bb58f..0394b0a 100644 ---- a/Makefile -+++ b/Makefile -@@ -35,31 +35,31 @@ distrib : - # Individual executables - # ---------------------- - anglen : anglen.o -- $(F77) $(FOPTS) -o $@ anglen.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o - clean : clean.o -- $(F77) $(FOPTS) -o $@ clean.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o - rmsdev : rmsdev.o -- $(F77) $(FOPTS) -o $@ rmsdev.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o - secstr : secstr.o -- $(F77) $(FOPTS) -o $@ secstr.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o - gfac2pdb : gfac2pdb.o ps.o -- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o - pplot : pplot.o ps.o -- $(F77) $(FOPTS) -o $@ pplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o - bplot : bplot.o ps.o -- $(F77) $(FOPTS) -o $@ bplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o - tplot : tplot.o ps.o -- $(F77) $(FOPTS) -o $@ tplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o - mplot : mplot.o ps.o -- $(F77) $(FOPTS) -o $@ mplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o - vplot : vplot.o ps.o -- $(F77) $(FOPTS) -o $@ vplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o - viol2pdb : viol2pdb.o ps.o -- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o - wirplot : wirplot.o ps.o -- $(F77) $(FOPTS) -o $@ wirplot.o ps.o -+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o - nb : nb.c -- $(CC) $(COPTS) -o nb nb.c $(CLIBS) -+ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS) - - # Individual rules for FORTRAN files with .inc files - # -------------------------------------------------- diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/procheck/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild deleted file mode 100644 index 3db0e3f24244..000000000000 --- a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit fortran-2 multilib toolchain-funcs versionator - -DESCRIPTION="Checks the stereochemical quality of a protein structure" -HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK" -SRC_URI=" - ${P}.tar.gz ${P}-README - doc? ( ${P}-manual.tar.gz )" - -LICENSE="procheck" -SLOT="0" -KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc" - -RDEPEND="app-shells/tcsh" -DEPEND="${RDEPEND}" - -RESTRICT="fetch" - -S="${WORKDIR}/${PN}" - -pkg_nofetch() { - elog "Please visit https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" - elog "and follow the instruction for downloading." - elog "Files should be renamed in the following way before being copied to your" - elog "DISTDIR directory:" - elog " ${PN}.tar.gz -> ${P}.tar.gz" - elog " README -> ${P}-README" - use doc && elog " manual.tar.gz -> ${P}-manual.tar.gz" -} - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-close.patch -) - -src_compile() { - emake \ - F77="$(tc-getFC)" \ - CC="$(tc-getCC)" \ - COPTS="${CFLAGS}" \ - FOPTS="${FFLAGS} -std=legacy" -} - -src_install() { - for i in *.scr; do - newbin ${i} ${i%.scr} - done - - exeinto /usr/libexec/${PN}/ - doexe \ - anglen \ - clean \ - rmsdev \ - secstr \ - gfac2pdb \ - pplot \ - bplot \ - tplot \ - mplot \ - vplot \ - viol2pdb \ - wirplot \ - nb - dodoc "${DISTDIR}"/${P}-README - - insinto /usr/libexec/${PN}/ - doins *.dat *.prm - newins resdefs.dat resdefs.data - - cat >> "${T}"/30${PN} <<- EOF - prodir="${EPREFIX}/usr/libexec/${PN}/" - EOF - - doenvd "${T}"/30${PN} - - if use doc; then - pushd "${WORKDIR}" > /dev/null - docinto html - dodoc -r manual - popd > /dev/null - fi -} diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest index dc5a1eddff6a..2c45708435b7 100644 --- a/sci-chemistry/propka/Manifest +++ b/sci-chemistry/propka/Manifest @@ -1,3 +1,5 @@ DIST propka-3.4.0.gh.tar.gz 363641 BLAKE2B 87f495ba69028593cf3ebf98ed33da0944f7a3833f2d08cae4f0a0b5cbe2f3a67e9812685b896a7d89c88ba25653861f135dbac53dc6df7af426a290bacb3d22 SHA512 2ce431c66374d0692acb7504661caa870ab6460ace3a6478f88c1d46a7bfcd82c748bf153a1ce2ea6d1611bc4bbf2351c4f5149f4578e5f8a9f9ec8385298fe9 +DIST propka-3.5.1.gh.tar.gz 376176 BLAKE2B ef4f5f51a6d08da566aa8dc4d2ec73ca028137031dbe49ca329589fe9ceb7cdda672cac755735a11bed79db1f31be5401b083239214177c2d459207ae998ae29 SHA512 3a9a7fd773700850f14c3ef1cc4ef7614242ea1191001fdca6afd44953486f208cbc067b84752c89e97e82ef6bac5561907b2aeafbee80c4d83cbf3ab443aaa2 EBUILD propka-3.4.0.ebuild 750 BLAKE2B 811914f17aaa8c9ba8779d4267ecc372c7397394ccf87bb6ea25159759248861da362c13d1e70a991ddd08783c9d4c8c9edb59b99aaac0e253f99935ed2666ee SHA512 e5d23bb7cff54dfc009435da11de8f7e73e2da41e908d4efde1f722a15e2af2d3e5c126fdeb59c5177349a64e6fdeb18cd407a7bd9a6aad3cbeaa3ab6ec04312 +EBUILD propka-3.5.1.ebuild 751 BLAKE2B b3db6aebf5bcf519ae9f248b854d92defe476233d311601ac158763e07ed757ad74542ead5507f7d81de2f356c59efce29f8c501922de544189b51431595b5c8 SHA512 15ff70d3711166276c7b548ebddccf6684942d095fd941e093bd027d55d9bf632c70e50ed045e9a00f8a3ec577927018444c2b38f686c7e772894b01b3d6117d MISC metadata.xml 417 BLAKE2B 89fda735965e8ae53eb86dfd438137e7770718b5601d5cd753cce9a03001419e53404dde70fed53d37ccf407265ee387accb26640bb4fce479e01ff141702b70 SHA512 5a9f942fa28e679ee5e1795fddf91661c35c55df79e0d9b742353ad265057ceb030ef15d3bb218ad5e8217c61d462aa09206e261c14dc363e6d6bfc3d20c6500 diff --git a/sci-chemistry/propka/propka-3.5.1.ebuild b/sci-chemistry/propka/propka-3.5.1.ebuild new file mode 100644 index 000000000000..2c9eb2ee4f27 --- /dev/null +++ b/sci-chemistry/propka/propka-3.5.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes" +HOMEPAGE="https://github.com/jensengroup/propka" +SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +python_prepare_all() { + # Do not install the tests + sed -e "/exclude/s:scripts:\', \'tests:g" \ + -i setup.py || die + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index dbc27f448a0d..c2aeb2fb9df4 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,5 +1,5 @@ AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 -EBUILD pymol-3.0.0.ebuild 2831 BLAKE2B b277127a25bc4b292238b374bd6945e372bbdfc6a7855a3e03c7855dd49fb2c75f3b064fbeb783f6dfc838f3069aeb65139a23caecc858c6557eed34a40cd79e SHA512 890933535af6f7bb0f49b554e6f9ab5fc2134a04c163ef28c61e2fb351faa5fd3c5aa166dd8bc444d649dd5688f1c5a2579acfdaeca41b8ca3f1247f24027351 +EBUILD pymol-3.0.0.ebuild 2958 BLAKE2B 2eac68b0cf15c3369e243b7456e00b1c1119f0d8399bea7321794981f41911bd56bc10713c9102475a054e6a52353cef63c0f9416974bb1db5d91ddd9f6d2dfa SHA512 ca7a597cd909d5a04e77c0afb7e2c07413b13dd42d5788db97defabee23370695299e17193b431eb6190c87a0e06d8e741d2067de973652d1749b244cfeb0254 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild index 150f7732d930..b6ec9fbef1e3 100644 --- a/sci-chemistry/pymol/pymol-3.0.0.ebuild +++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild @@ -26,19 +26,20 @@ IUSE="+netcdf web" DEPEND=" dev-cpp/msgpack-cxx dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] + sys-libs/zlib media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) " -RDEPEND="${DEPEND} +RDEPEND=" + ${DEPEND} + media-video/mpeg-tools + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] sci-chemistry/chemical-mime-data " @@ -66,6 +67,11 @@ python_prepare_all() { } python_configure_all() { + # -Werror=odr + # https://bugs.gentoo.org/933235 + # https://github.com/schrodinger/pymol-open-source/issues/395 + filter-lto + use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) } diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest index 0d3471385728..46bf0037f904 100644 --- a/sci-chemistry/tinker/Manifest +++ b/sci-chemistry/tinker/Manifest @@ -1,4 +1,4 @@ AUX 8.2.1-openmp.patch 559 BLAKE2B 254a7b5d5d40bec938420527ad77e4ec96b9cee50392137eab3370df35a00a00b9488b5cd95c4e3c52d4904a6093216a782f52c82c2141cd913c6cf10f2fbcc7 SHA512 799b488ddba95ec75c2f5f97bdba10e297cad12d23239354b7d66af47b4e9ef1496e8f6b8a7446f85827a8303105af7552616bc865a4e8114b89d3e6e3302ed6 DIST tinker-8.2.1.tar.gz 33015410 BLAKE2B 0b7c94662248761459cf9d681056f5cf9c4d669a790a522f23f800bf355235f6a9f392e008b13d14cf1e17d9725abb6512077c24ff7772108d69c9cf35b43e6e SHA512 5039078781d1ce226456882dd95ad15715f1e91829d26efcdb29ceedc213973883699eb6710b0a162a74208809305b7fee734b175139e6df63d0460fe5751ae7 -EBUILD tinker-8.2.1-r1.ebuild 2387 BLAKE2B 2eec46ab90656d4336f4c130bac95f76aae850ce7bea72ce7ba5fde37897f4345c7ff8e714190dad5279592ad51fae37b5c96190614a67725d6f23c534ca94c3 SHA512 f89dcf18394067c9485fb8a85c8a6bd841bf485f3deb6671ed457e995bf008e6db64206b0903cda9e0e86dd4ffc9253ee2f1f8b469688d044e629c506a5c3abb +EBUILD tinker-8.2.1-r1.ebuild 2529 BLAKE2B 3ed97f45a8850f58cc79216127c51acca2d85f78f32e7d753e4e98e7a7bda004373664fe60cdd38f66b12d9f6c79fe70f1f78dd33d9ff27a9cca9373716e66a0 SHA512 cf263a10c4ff53074b4ecaa1c7f4fd936291043b0aafa47af25c371efd5a8b761e349e1d55bd65c03567b9970579996599657bda34bfb431a4918dcd7582defa MISC metadata.xml 349 BLAKE2B e2a70d46ddb77f5ea51a0d6d378cdcbe2c897464127bd86c34ec43615588a509ff038e035c24855c305248789eb0708d51d21208d2cc65e8507e4f767172582f SHA512 0cb63aaf7aadd62ea12289936ea25c8f5233c8784af96b71f103794d6bd7e0711b53728a2840f5768df2652c0b19e220b1f35223dbf27fc65f7871b6e3b4c756 diff --git a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild index 9964b16b549f..8689a962c2fd 100644 --- a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild +++ b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -50,6 +50,11 @@ src_prepare() { } src_compile() { + # tests fail with weird results under LTO + # https://bugs.gentoo.org/878059 + # https://github.com/TinkerTools/tinker/issues/159 + filter-lto + local javalib= _omplib _fftwlib for i in $(java-config -g LDPATH | sed 's|:| |g'); do [[ -f ${i}/libjvm.so ]] && javalib=${i} diff --git a/sci-chemistry/votca/Manifest b/sci-chemistry/votca/Manifest index f8eb4f2293fe..adcbcc0ddad3 100644 --- a/sci-chemistry/votca/Manifest +++ b/sci-chemistry/votca/Manifest @@ -1,4 +1,4 @@ DIST votca-2022.1.tar.gz 61692029 BLAKE2B c58023098f596d7c6f301e94883df3e442761b8c1009823ef5a07e788fabb2a0fa572326e0d614f8102104ef5dcec89505da1c911bb703126c123d2a25a2031e SHA512 dda5cbf1835440abd1b0b511275e10e5facfa9f133062ae082cca4f5654e4af0be0b574b87c70004c0d07920519927bac5620b89ce073de9985bdf792f0dd21a -EBUILD votca-2022.1-r1.ebuild 1871 BLAKE2B 52840f4654fba69077c0950ba5ffee7abb9c4cd0c937bfe3331aa70ec1e0dc44af2309ddba033a660f31d77ade08bd74da90551586d16ceb4d71aa2894a1d7b0 SHA512 ea82eb9c580ff6e5337bf1d96d3c8c716d207d5515df03c466e3a775a89aeba59bc533ee3f047cae23bcefc3653c3a4f98cf752ca4585e7cbe61bab1a6059239 -EBUILD votca-9999.ebuild 1872 BLAKE2B cf72b8d2731e2dd7a11609a760bcdd918579eca872c8ffdc96931220df192d14e535b7a2c4e23861a44a0fa3acd56c5a0e65a324adf9322ecf7d79ebb0916f02 SHA512 7f068a887eb57eba03b83589cb474a5269179233b300f5f3c861a21f9aa40397ed8407cb89046c19f6ea42b89ae51b3b83e43fd73dd9c78952fbbf2aac0127a9 +EBUILD votca-2022.1-r1.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c +EBUILD votca-9999.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c MISC metadata.xml 465 BLAKE2B 3fe0aa7dbb87cfe5ec1b5d1500dccb087f2f582982ab7d41687675f7ad38ce3eae1c12141ab8a020d467114cc7017da64ceaa65a10bb37f55ff3aed3e113378b SHA512 b204a6c45aea2fc428a0e421cfc22a218e59ef4f9cb8e352bdf8983272c9f28baf2beec4650ca65e8fb640d713dbdb39d2f43b1ccfce8329b0c3669e6b4562c8 diff --git a/sci-chemistry/votca/votca-2022.1-r1.ebuild b/sci-chemistry/votca/votca-2022.1-r1.ebuild index ad5aa680498e..88d3c6a469fb 100644 --- a/sci-chemistry/votca/votca-2022.1-r1.ebuild +++ b/sci-chemistry/votca/votca-2022.1-r1.ebuild @@ -1,8 +1,8 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{9..11} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..12} ) inherit bash-completion-r1 cmake python-single-r1 diff --git a/sci-chemistry/votca/votca-9999.ebuild b/sci-chemistry/votca/votca-9999.ebuild index 04064219f641..88d3c6a469fb 100644 --- a/sci-chemistry/votca/votca-9999.ebuild +++ b/sci-chemistry/votca/votca-9999.ebuild @@ -1,8 +1,8 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{9..10} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..12} ) inherit bash-completion-r1 cmake python-single-r1 @@ -16,7 +16,7 @@ else MY_PV="${PV}" fi SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux" + KEYWORDS="amd64 ~x86 ~amd64-linux" S="${WORKDIR}/votca-${MY_PV}" fi diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest deleted file mode 100644 index d49a26f26741..000000000000 --- a/sci-chemistry/xyza2pipe/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX xyza2pipe-20121001-gentoo.patch 3974 BLAKE2B cf3f4b58c6348a6295b7874ca20d7d88f6477e1174b54bac7089898ff7509fbf07d8d34aab2d333059c67f7ccc9d1b99e4e40c9bfd8a327f600fc4578a2f1a06 SHA512 7b8be1fd799d65e9a600766afb21e95a4722eff8a657f88d0adaf5aaf11ed369f6d8a27f3e003337570837abc45cfa9e758d1219af275773f79b81d1c1c322c4 -DIST xyza2pipe-20121001.tgz 61002 BLAKE2B 648e65b63cc0b363dd0087b7ef64a1e287654a165baaf7d967821f11cffb70dd7f0da864dfa3b915553546c8cbbc83fda411d9b979551d3d72334db6580e5d64 SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855 -EBUILD xyza2pipe-20121001.ebuild 682 BLAKE2B a1cbd50a946dc37ab1e55f998b2ad6631e53fd6138f886009ef28e4a121721c5a8e6ffcdd0d79c4b387e2016b456c14d9b3db039f95bd6d6c85f774d8fff71b2 SHA512 4253c166e0a2101b3a5b91aed25193107d588cfbc3db07b66f64ab98bb2888a5e3342d093db15c9686be6519d3ad3372cd6b53f52a4091ee35a458d210c428e6 -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch deleted file mode 100644 index ec4220dd0695..000000000000 --- a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch +++ /dev/null @@ -1,168 +0,0 @@ - Makefile | 106 +++++++++++++++++++++++++++++++++++++-------------------------- - 1 file changed, 63 insertions(+), 43 deletions(-) - -diff --git a/Makefile b/Makefile -index 15d4bd3..e738ec2 100644 ---- a/Makefile -+++ b/Makefile -@@ -4,7 +4,7 @@ - # Last modified: Feb/22/2012 - # - --CFLAGS = -O3 -+CFLAGS ?= -O3 - MFLAGS = -lm - - TARGETS = xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\ -@@ -62,89 +62,109 @@ clean: - rm -f $(TARGETS) addxyza2pipe - - $(OBJECTS_MATH): -- $(CC) $*.c -c -o $@ $(CFLAGS) -D__XYZA2PIPE__ -+ $(CC) $(CPPFLAGS) -D__XYZA2PIPE__ $(CFLAGS) $*.c -c -o $@ - - .o: -- $(CC) $< -c -o $@ $(CFLAGS) -+ $(CC) $(CPPFLAGS) $(CFLAGS) $< -c -o $@ - - xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - nv2pipe: $(OBJECTS_C) $(OBJECTS_NP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2nv: $(OBJECTS_C) $(OBJECTS_PN) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - azara2pipe: $(OBJECTS_C) $(OBJECTS_AP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2azara: $(OBJECTS_C) $(OBJECTS_PA) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - add2pipe: $(OBJECTS_C) $(OBJECTS_DXP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - rm -f addxyza2pipe - ln -s add2pipe addxyza2pipe - - adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ - - addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP) -- $(CC) $@.c $^ -o $@ \ -- $(CFLAGS) $(MFLAGS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ -+ $(MFLAGS) -+ mv -v $@ bin/ diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/xyza2pipe/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild deleted file mode 100644 index e6ba5c19332f..000000000000 --- a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Cross conversion environment of NMR spectra" -HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src" -SRC_URI="http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz -> ${P}.tgz" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="olivia" -IUSE="" - -S="${WORKDIR}"/${PN} - -PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) - -src_prepare() { - default - tc-export CC - mkdir bin || die -} - -src_install() { - local i - dodoc README FEEDBACK - cd bin || die - for i in *; do - newbin ${i}{,-olivia} - done -} |