From d934827bf44b7cfcf6711964418148fa60877668 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 25 Nov 2020 22:39:15 +0000 Subject: gentoo resync : 25.11.2020 --- sci-biology/Manifest.gz | Bin 23336 -> 22478 bytes sci-biology/amos/Manifest | 8 - sci-biology/amos/amos-3.1.0-r4.ebuild | 52 -- .../amos/files/amos-3.1.0-fix-build-system.patch | 116 ---- sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 - ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 - sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch | 136 ----- sci-biology/amos/metadata.xml | 11 - sci-biology/clustalw-mpi/Manifest | 7 +- .../clustalw-mpi/clustalw-mpi-0.13-r2.ebuild | 39 -- .../clustalw-mpi/clustalw-mpi-0.13-r3.ebuild | 42 ++ sci-biology/clustalw-mpi/files/0.13-gentoo.patch | 23 - .../files/clustalw-mpi-0.13-fno-common.patch | 13 + .../files/clustalw-mpi-0.13-makefile.patch | 23 + sci-biology/clustalw-mpi/metadata.xml | 18 +- sci-biology/dialign-tx/Manifest | 5 +- 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--git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 4c7f9b88e8d6..9603eb7f0869 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest deleted file mode 100644 index 0749a737c777..000000000000 --- a/sci-biology/amos/Manifest +++ /dev/null @@ -1,8 +0,0 @@ -AUX amos-3.1.0-fix-build-system.patch 3132 BLAKE2B a7758991b5916cec6e9a2a39ee55beef73d14c19b7154ab2ced8e41eca411d1b6cacda5b7388e3ee48f330e489e4012660b3c08383c423a8553d283cd1cc4764 SHA512 b23c168c166f8a1dad89d1b25536a59be3e68a6478cef3db5664dc901cef0547213a8622a72ee1a2e1d5b8930c65d95e309573f903423e8fb80fb7312d89f863 -AUX amos-3.1.0-gcc-4.7.patch 400 BLAKE2B af160452d1bf52df204156dc9039645483c0ee349b96c2562eba4608695ac76b308c9cc2bc82a55401b3d56c33c4d2bae9e07a0a62ed4a3b15becb8f95ecda7f SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835 -AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da762750140f8880968c952b275d625f92b43ee8c35aaa23b687cc8d6cda441aa7b7cc883a67efe2a0d4a9cc13ee9f6b3663fef9f8274693350fe8e87 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f -AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe -DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 -DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 -EBUILD amos-3.1.0-r4.ebuild 1110 BLAKE2B 4730d6a04ba727fd72ea825c6c57d65079ae9ddb29411f0a26aa94653309364ddec742104783044549adc2a60f06a7452f76e392145aa02db472042dde05e1d5 SHA512 7cb40d45dabc4e6cc188d3edf8347f34578d1f955b2d522273f3b551be6974023145e35a443f0e4495d70746aa40b6c451cedf999c102f1f8f7ffbab09748d61 -MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497 diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild deleted file mode 100644 index 0dbcaffd81da..000000000000 --- a/sci-biology/amos/amos-3.1.0-r4.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="" -RDEPEND="${DEPEND} - ${PYTHON_DEPS} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch - "${WORKDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-qa-Wformat.patch - "${FILESDIR}"/${P}-fix-build-system.patch -) - -src_prepare() { - default - eautoreconf - - # prevent GCC 6 log pollution due - # to hash_map deprecation in C++11 - append-cxxflags -Wno-cpp -} - -src_configure() { - econf --with-qmake-qt4=no -} - -src_install() { - default - python_fix_shebang "${ED%/}"/usr/bin/goBambus2 -} diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch deleted file mode 100644 index 9c824dd2f122..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch +++ /dev/null @@ -1,116 +0,0 @@ -* Use proper AR and not just 'ar' -* Fix build system to build in parallel - ---- a/configure.ac -+++ b/configure.ac -@@ -34,6 +34,7 @@ - AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_RANLIB -+AM_PROG_AR - AC_PROG_CPP - AC_PATH_PROG(PERL, [perl], [:]) - AC_PATH_PROG(PYTHON, [python], [:]) ---- a/src/Align/Makefile.am -+++ b/src/Align/Makefile.am -@@ -133,7 +133,7 @@ - - ##-- hash-overlap - hash_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -172,7 +172,7 @@ - - ##-- make-consensus - make_consensus_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -182,7 +182,7 @@ - - ##-- make-consensus_poly - make_consensus_poly_LDADD = \ -- $(top_builddir)/src/Align/libAlign_poly.a \ -+ libAlign_poly.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -192,7 +192,7 @@ - - ##-- maligntest - maligntest_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -202,7 +202,7 @@ - - ##-- merge-contigs - merge_contigs_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -235,7 +235,7 @@ - - ##-- show-ma-asm - show_ma_asm_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a - show_ma_asm_SOURCES = \ -@@ -261,7 +261,7 @@ - - ##-- simple-overlap - simple_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -272,7 +272,7 @@ - - ##-- test-align - test_align_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ ---- a/src/Bambus/Bundler/Makefile.am -+++ b/src/Bambus/Bundler/Makefile.am -@@ -47,7 +47,7 @@ - clk.cc - - MarkRepeats_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -55,7 +55,7 @@ - MarkRepeats.cc - - OrientContigs_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -63,7 +63,7 @@ - OrientContigs.cc - - FilterEdgesByCluster_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch deleted file mode 100644 index de2a41184c52..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/Align/find-tandem.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc -index ddf1cab..a29e21e 100644 ---- a/src/Align/find-tandem.cc -+++ b/src/Align/find-tandem.cc -@@ -7,6 +7,7 @@ - #include - #include - #include -+#include - using namespace std; - - const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch deleted file mode 100644 index 97a8f59d0208..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch +++ /dev/null @@ -1,25 +0,0 @@ ---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 -+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 -@@ -1,7 +1,7 @@ - #pipeline script for assembly + Bambus 2 - #contributed by Todd J Treangen - --import string, sys, os, subprocess#, spincursor -+import sys, os, subprocess#, spincursor - - RED = "\033[0;31m" - GREEN = "\033[0;32m" -@@ -360,7 +360,7 @@ - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) - -- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) -+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) - - if xopt_dict["verbose"] == 1: - print "10) running OutputResults" -@@ -388,4 +388,3 @@ - else: - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) --) diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch deleted file mode 100644 index 13f4eeb247a1..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch +++ /dev/null @@ -1,136 +0,0 @@ -Fix QA warnings, due to using incorrect format specifiers in printf: -* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’, -* but argument 3 has type ‘std::vector::size_type {aka long unsigned int}’ [-Wformat=] -* fprintf (stderr, "%u b contigs\n", b . size ()); - ---- a/src/Align/align.cc -+++ b/src/Align/align.cc -@@ -1936,7 +1936,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - - for (i = 0; i < n; i ++) - { -@@ -3936,7 +3936,7 @@ - } - - // Array of sum of quality scores in the slice for A,C,G,T,- resp. -- for (j = 0; j < 6; j ++) -+ for (j = 0; j < 5; j ++) - qvsum [j] = 0; - - int nof_ambiguities = 0; ---- a/src/Align/align_poly.cc -+++ b/src/Align/align_poly.cc -@@ -1761,7 +1761,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - for (i = 0; i < n; i ++) - { - fprintf (fp, "\nString #%d:\n", i); ---- a/src/Align/count-qmers.cc -+++ b/src/Align/count-qmers.cc -@@ -191,8 +191,8 @@ - - PrintMers(mer_table, min_count); - -- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT); -- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN); -+ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT); -+ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN); - } - catch (Exception_t & e) - { ---- a/src/Align/kmer-cov.cc -+++ b/src/Align/kmer-cov.cc -@@ -485,7 +485,7 @@ - Kmer_Len = s . length (); - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/kmer-cov-plot.cc -+++ b/src/Align/kmer-cov-plot.cc -@@ -316,7 +316,7 @@ - } - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/make-consensus.cc -+++ b/src/Align/make-consensus.cc -@@ -303,7 +303,7 @@ - break; - } - -- sprintf (sid, "%ld", ++layout_id); -+ sprintf (sid, "%u", ++layout_id); - cid = string (sid); - ID_t lid = layout.getIID (); - if (lid == 0) ---- a/src/Align/make-consensus_poly.cc -+++ b/src/Align/make-consensus_poly.cc -@@ -279,7 +279,7 @@ - break; - } - -- sprintf(sid, "%ld", ++layout_id); -+ sprintf(sid, "%u", ++layout_id); - cid = string(sid); - ID_t lid = layout.getIID(); - if (lid == 0) { ---- a/src/Align/simple-overlap.cc -+++ b/src/Align/simple-overlap.cc -@@ -422,7 +422,7 @@ - "Options:\n" - " -a Also show alignments of overlaps \n" - " -E Maximum error rate for overlaps is \n" -- " e.g., -E 0.06 for 6% error rate\n" -+ " e.g., -E 0.06 for 6%% error rate\n" - " -F Input is a fasta file\n" - " -h Print this usage message\n" - " -o Set minimum overlap length to \n" ---- a/src/Compare/contig-cmp.cc -+++ b/src/Compare/contig-cmp.cc -@@ -145,7 +145,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u a contigs\n", a . size ()); -+ fprintf (stderr, "%zu a contigs\n", a . size ()); - vector a_contig (max_id + 1); - n = a . size (); - for (i = 0; i < n; i ++) -@@ -234,7 +234,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u b contigs\n", b . size ()); -+ fprintf (stderr, "%zu b contigs\n", b . size ()); - vector b_contig (max_id + 1); - n = b . size (); - for (i = 0; i < n; i ++) ---- a/src/Staden/progs/trace_convert.c -+++ b/src/Staden/progs/trace_convert.c -@@ -6,6 +6,9 @@ - #include "traceType.h" - #include "seqIOABI.h" - -+#include -+#include -+ - static char fileIdentifier[] = "$Id$"; - - struct opts { diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml deleted file mode 100644 index 2668bce2ac8a..000000000000 --- a/sci-biology/amos/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - amos - - diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest index 3088142ea209..23d86f7036f9 100644 --- a/sci-biology/clustalw-mpi/Manifest +++ b/sci-biology/clustalw-mpi/Manifest @@ -1,4 +1,5 @@ -AUX 0.13-gentoo.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8 +AUX clustalw-mpi-0.13-fno-common.patch 449 BLAKE2B e1d8e7cd34e5fea17fb883861e2cb32874c34340b37f6d2983688930706b41cf1a7653b73d3860b8b5adcdca353b7a9ec94d9bda5090048d040dc6eb2b1a3d6b SHA512 71ea0f57c7235bc99f3e0d364476c268a27d2eeaba8e9bbcc01eceb0c84b1aabd0d9ce66dd738e6b0e75919f6cc18890e4dde7be6097e0e3051a9907bee56b4f +AUX clustalw-mpi-0.13-makefile.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8 DIST clustalw-mpi-0.13.tar.gz 154911 BLAKE2B 705f62263340b0ac13895657c97e185f395910f25653bdcc20cf867732c270c65eebebe5b914367a534a5d058909d0baf307c0a3727a2095d4f21c313e83b94d SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df -EBUILD clustalw-mpi-0.13-r2.ebuild 962 BLAKE2B bcc71a3c09ae2d9e3c4f41b6a4e0771dd778c3cbdcf650cb9319124834a02d40b129757675ea060b6d39c699d3b123b757129f08b8d98c65b619b74467d8bd4b SHA512 48cd3c0ff42cf9c5185e70d0fbdb1b21020a7ad75156adba06346b7cd6847dfbb2752164edd93238890ef55d38565cdcc196355094ca3e8e253f3d508b409ef3 -MISC metadata.xml 491 BLAKE2B b65663a63fa098ac80bc0226163188776cb7805688651ea22724ed457924a3d970e5e368210a994f536f9152b3af2766d07c1eefb8b620299c3e1efffda840c3 SHA512 d242bee2ea381f992deb30b406b89ec2da08e1d513da5d9a94016ea07247670744d25bac8175607291c39d80090d3d1746154d3c60ba95bdd720d57c0212b3d0 +EBUILD clustalw-mpi-0.13-r3.ebuild 1012 BLAKE2B e1ae0c2237433f8826bcc66b6c3b11e8313a41ddb8201a6ffbb1300b7f9bfbb45c568e9903f9296ca97f54a9aec98199c2c9e4f942b43e89cfaff4fe982d7472 SHA512 9b5af106fa5daed7ff7c6ab49037ca82b42ce781138fa076efaf43f70b09ebfdcd45dc5e63d53a95a9414ca273260ebe5971664559001499cba8eefb80e26694 +MISC metadata.xml 487 BLAKE2B 7ca9b9cccd9bf7468703e755d4090e077a975c6463d97c612be7508ec38497d391e10fa5a50d5e76fc1f94f735b4062a4ea894d588706092166339c2046410f3 SHA512 4b7038b53d689f5a2e0f6a0b121235efb6d5c6fa9b8586107071f7820b0c2d9274a3b8b533afc84709df408751addf2b2408850542ed0083f47c7220d4bc61f5 diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild deleted file mode 100644 index 76d3b80cde32..000000000000 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm" -HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" -SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="mpi_njtree static_pairalign" - -DEPEND="virtual/mpi" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) - -src_prepare() { - default - - if use mpi_njtree; then - sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ - die "Failed to configure MPI code for NJ trees" - fi - - if use static_pairalign; then - sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ - die "Failed to configure static scheduling for pair alignments" - fi -} - -src_install() { - dobin ${PN} - newdoc README.${PN} README -} diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild new file mode 100644 index 000000000000..334c34e78ce6 --- /dev/null +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm" +HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" +SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="mpi-njtree static-pairalign" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_prepare() { + default + + if use mpi-njtree; then + sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ + die "Failed to configure MPI code for NJ trees" + fi + + if use static-pairalign; then + sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ + die "Failed to configure static scheduling for pair alignments" + fi +} + +src_install() { + dobin clustalw-mpi + newdoc README.clustalw-mpi README +} diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch deleted file mode 100644 index 6e36061cbb39..000000000000 --- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch +++ /dev/null @@ -1,23 +0,0 @@ - Makefile | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Makefile b/Makefile -index f2107ce..835232b 100644 ---- a/Makefile -+++ b/Makefile -@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE - PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN - #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN - --CFLAGS = -c -O3 -+CFLAGS += -c - #CFLAGS = -c -O3 -funroll-all-loops --LFLAGS = -lm -+LIBS = -lm - - clustalw-mpi: $(OBJECTS) -- $(CC) -o $@ $(OBJECTS) $(LFLAGS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) - - interface.o : interface.c $(HEADERS) param.h - $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch new file mode 100644 index 000000000000..da74f0ba172d --- /dev/null +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch @@ -0,0 +1,13 @@ +--- a/parallel_compare.c ++++ b/parallel_compare.c +@@ -74,8 +74,8 @@ + static sint **accum; + static sint *diag_index; + static char *slopes; +-sint ktup,window,wind_gap,signif; +-sint *zza, *zzb, *zzc, *zzd; ++extern sint ktup,window,wind_gap,signif; ++extern sint *zza, *zzb, *zzc, *zzd; + extern Boolean percent; + static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l); + static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len); diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch new file mode 100644 index 000000000000..6e36061cbb39 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch @@ -0,0 +1,23 @@ + Makefile | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index f2107ce..835232b 100644 +--- a/Makefile ++++ b/Makefile +@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE + PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN + #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN + +-CFLAGS = -c -O3 ++CFLAGS += -c + #CFLAGS = -c -O3 -funroll-all-loops +-LFLAGS = -lm ++LIBS = -lm + + clustalw-mpi: $(OBJECTS) +- $(CC) -o $@ $(OBJECTS) $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml index 8ab4494152c8..ffe2c4efec87 100644 --- a/sci-biology/clustalw-mpi/metadata.xml +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -1,14 +1,12 @@ - - sci-biology@gentoo.org - Gentoo Biology Project - - - Use MPI (as opposed to serial) code for computing - neighbor-joining trees - Use static (as opposed to dynamic) scheduling - for pair alignments - + + sci-biology@gentoo.org + Gentoo Biology Project + + + Use MPI (as opposed to serial) code for computing neighbor-joining trees + Use static (as opposed to dynamic) scheduling for pair alignments + diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest index 443791cbbb26..ec6b81e67ea3 100644 --- a/sci-biology/dialign-tx/Manifest +++ b/sci-biology/dialign-tx/Manifest @@ -1,7 +1,8 @@ AUX dialign-tx-1.0.2-fix-build-system.patch 588 BLAKE2B 3d9757b2b66497a47bfc3412a1e014f85e0dd12c2247103c813f3406ae0b34e8ba8a68cf31481f9f184095c07e63840fa2643c04a34a3e3f2605b90b2e8bba50 SHA512 30a474f59fb18dcef572299aa6bb6a22d9d6188193a3341bd04c32d6c388358e890ea17bcb8fd31fe80cee58330be6cb004b5936bf98d204e6f5a1e40627bf4f -AUX dialign-tx-1.0.2-gnu89-inline.patch 493 BLAKE2B d37822818faabfa55cfd0a32cf0c0f22548ff29eb7c55712b1ef8e4fe4652531cfe821236e206a7bdaec74c4cac22e5d519be41f282b717d2119d7a79e478e44 SHA512 ad63585d93a10b44b1ca810b4a1bbbd991cc5fb1e762b941931d28f50dcc6a2bb6fdedea7c5faedcf4b2452dc8b99374423752694c5aa0a481ce5e97d8f5d3dd +AUX dialign-tx-1.0.2-fno-common.patch 556 BLAKE2B d77bf94e61f376548f66776bde79081d18798d0645ec75fd314ac1394059e3498e20f638553b484e5e077cf5c253138ff57842920ce8237b63c4e799e51951cf SHA512 03b028cf2f0bf1b8e67bbc24fbbefc652ce2bd2de89aece26b32c6e2c86b8639cdbcf24e8a6a77ad31b690b5586f262affe39111483677372b547879207eacc3 +AUX dialign-tx-1.0.2-gnu89-inline.patch 1406 BLAKE2B 6a97e3300a730a87db721572fe6f4729b9915746d68f4b911ebe0d8ee91adade8b5584da39f1fdc549d6cbb0cbb941fddb4e63f669197a8761ee680bd35d9bac SHA512 55125d6634704cc2bfa4b44f502998bfb6e051190d398c8f3d3e9d48256b3f7fb2c9e54500e8c6d01493f2f501caaf12d7f0954c1e6ab455201ac2b507f43069 AUX dialign-tx-1.0.2-implicits.patch 780 BLAKE2B b6eb50c7eaecf6439a1d27a0173661efef100a10976abf521fe50a4687d7e89e0cb094693118a84e68daae3918708ee3323073299d3d28786031a1f41c39af75 SHA512 783afc4527e0a77f0aac66bd8aa00ce3e5ddd81dd652c7459e551c609755eb3b0bd5b02566d8d1636b8840ed8567bb5652866c41ecf038ac9fe5682e1edf3e64 AUX dialign-tx-1.0.2-modernize.patch 6149 BLAKE2B f6f3044b38d4652c2bc3aa63714beb42220ac00d0ecfe68b692b7af0f6dc1d29a8d053962d324e33bf32df2b92bd0fad40b5ec352ae837f6eaba1920f73d8d90 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a DIST DIALIGN-TX_1.0.2.tar.gz 1765296 BLAKE2B 3cce811a58fcf210f42c4a783e8ebb56c66436912ff04bce270058193f0d7b21114d75e2d67829c7abfbb35814e5a16f7f952611729ab211d066403a411db94a SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 -EBUILD dialign-tx-1.0.2-r2.ebuild 950 BLAKE2B 127ba32952e662b90c43dd901f4fe8aa1f6bb99d57adfc39b3bc65dfc9b52ece3809386b3fa2bf4ee649c83b5cc93306930b995ced48f586edbbb85c551a55d2 SHA512 813f6a5337e0c390ef57eedbbb80b9553f0f9bc81fbdbed58d4572e7a3d8d830b15ed54aa9033fadfa49157fcee94ec43396b9cd1c03d9889079fb2d4267cf15 +EBUILD dialign-tx-1.0.2-r2.ebuild 999 BLAKE2B 4fe11a5ee9d9fbb624911096f9a326dd0431bcf9f5e314ec9b551dbd1772284527e5f6ea4344a3698e337c4fbd75f631c72fb8c248d451902f9cb68b0d7d55fd SHA512 d8df0ccec568af8b0671101af9a7a88b7f52bcbe7095700fbc4e32c238bb464a9d213c90ab162195685361fb60f035ac7f8fbdf580633a32315005fd7378ab4d MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild index 123977916f06..78681265a0b7 100644 --- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -15,12 +15,13 @@ LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86" -S=${WORKDIR}/${MY_P} +S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-implicits.patch "${FILESDIR}"/${P}-modernize.patch "${FILESDIR}"/${P}-gnu89-inline.patch + "${FILESDIR}"/${P}-fno-common.patch ) src_configure() { @@ -34,12 +35,12 @@ src_compile() { src_install() { dobin source/dialign-tx - insinto /usr/$(get_libdir)/${PN}/conf + insinto /usr/$(get_libdir)/dialign-tx/conf doins -r conf/. } pkg_postinst() { einfo "The configuration directory is" - einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf" - einfo "You will need to pass this to ${PN} on every run." + einfo "${EROOT}/usr/$(get_libdir)/dialign-tx/conf" + einfo "You will need to pass this to dialign-tx on every run." } diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch new file mode 100644 index 000000000000..de3104fa0ebb --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch @@ -0,0 +1,22 @@ +--- a/source/parameters.c ++++ b/source/parameters.c +@@ -26,6 +26,8 @@ + + extern char *optarg; + extern int optind, opterr, optopt; ++ ++struct parameters* para; + /**************************** + * PROTEIN DEFAULT VALUES! * + ****************************/ +--- a/source/parameters.h ++++ b/source/parameters.h +@@ -138,7 +138,7 @@ + /* global variable */ + /* */ + /************************************************/ +-struct parameters* para; ++extern struct parameters* para; + + + diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch index 21f576f07052..fc8d0284e6ab 100644 --- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch @@ -1,5 +1,25 @@ +--- a/source/assemble.c ++++ b/source/assemble.c +@@ -574,7 +574,7 @@ + * returns a value <0 if there is an non-conflicting overlap + * returns 0 in all other non-conflicting cases + */ +-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { ++static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { + // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!"); + int s1_1 = dg1->seq_p1.num; + int s1_2 = dg1->seq_p2.num; --- a/source/diag.c +++ b/source/diag.c +@@ -312,7 +312,7 @@ + /** + * calculates the overlap weight for the given diag + */ +-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ++void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist) { + int sn1 = dg->seq_p1.num; + int sn2 = dg->seq_p2.num; @@ -958,7 +958,7 @@ * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest index fd37224607b6..abf651b02922 100644 --- a/sci-biology/embassy-emnu/Manifest +++ b/sci-biology/embassy-emnu/Manifest @@ -1,4 +1,4 @@ -AUX embassy-emnu-1.05.650_fix-build-system.patch 4072 BLAKE2B d256a82e214b8900eaab252e6695c4120eabb8379a59cfffe6a8b70e5decaf681af42ed9de3f9f74215a1a7f21e11367763aa705d7495eca41ab3fea1483e056 SHA512 644c4f0930a157ae9121354b49ddeb756b25d823d25733405fcc500d2080067f013443ba43a1512c6940fc4fd19cfe38c336dd0c58237354bad580cf9ba68b2e +AUX embassy-emnu-1.05.650_fix-build-system.patch 3844 BLAKE2B b77be3d3917db4cdfcfce201089595a80b970575f77dffbc366c77ae27010b9a78582b035728008b20ae11b0c7c18b7b20a5fdfcd59b840f85f54a1db2fc5496 SHA512 1836ba79762f62f9e27a770a35b89ae5f2821c4d23dc93b1ab3505404105280256f1c43287471385a5be71659fbe614f5f7f97d78a4743b3b1b90b303a25f674 DIST embassy-emnu-1.05.660.tar.gz 425595 BLAKE2B ed6ab4a0572ac4b57cf0f0b75a3894b1f950f7f373a7c6797ea0c34ba1b0d0e044f2c6951aec7c084340c6b207aa4c8b386055e92ceb9fc83c920fc70e83e665 SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd EBUILD embassy-emnu-1.05.660.ebuild 470 BLAKE2B 4a5fb352f30c729ded48ba438d978ff7ba85ee419eb1dbe94df07f34dd2b6fa50527615678c166cd627090bb2b15bd88d6d8ffd3d66e16006714d9a175444dec SHA512 ec9df242ed5a421fdbc45b59c1a9a9a3cfe540bde2ea010a29ac56e758d26fa0f1a1c850de644e82486a574850b0702d7d87adebfd851cd40076e17596c88f05 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch index 4e14bac1704a..ecd7f928da3a 100644 --- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 67 +++++++++++--------------------------------------- - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 7 +++--- - 3 files changed, 18 insertions(+), 58 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 7482ade..b815bdb 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 7482ade..b815bdb 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 7482ade..b815bdb 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,23 +70,24 @@ index 7482ade..b815bdb 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -899,20 +864,16 @@ dnl fi +@@ -899,20 +864,16 @@ dnl emnu and mse only: uses curses -dnl Test if --with-curses is given -AC_ARG_WITH([curses], -[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) -+dnl Test if --enable-curses is given -+AC_ARG_ENABLE([curses], -+[AS_HELP_STRING([--enable-curses], [curses])]) - +- -AC_MSG_CHECKING([for curses]) - -AS_IF([test "${with_curses}"], -[ - CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" - LDFLAGS="$LDFLAGS -L${with_curses}/lib" ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ +AS_IF([test "x$enable_curses" = "xyes"], [ + PKG_CHECK_MODULES([NCURSES], [ncurses]) + PKG_CHECK_MODULES([FORM], [form]) @@ -105,8 +99,6 @@ index 7482ade..b815bdb 100644 -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -114,11 +106,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index b295079..330c76f 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,8 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -130,10 +120,21 @@ index b295079..330c76f 100644 endif if ISSHARED -@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +33,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -56,6 +55,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) endif diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest deleted file mode 100644 index b52ed7b5f840..000000000000 --- a/sci-biology/embassy-meme/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX embassy-meme-4.7.650_fix-build-system.patch 2860 BLAKE2B 4b6d608d6fde975acd09373b39c64449585cd5f76e323fdd07c9ee9f741cf0f679a143bdd8ef110a0d93b70451425cf021b763860ef376b03c13f8a9456f8e62 SHA512 c44b219c75e67d17fcfd56145ae3709053bda38b8690141d1e9b846e4e4a9cab135f0dc9c5399e4712cf030ad562dd075f45c393e78157a2c1b92d80903b3d1c -DIST embassy-meme-4.7.660.tar.gz 622448 BLAKE2B 93bbbe3de085aa2cd843349f8397b2d1f547be62afdb7deb30eec90a891f7825c847b92754bd956388b1bfe0250cabcbc7ad68f7d0378748a7949001016d344c SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f -EBUILD embassy-meme-4.7.660.ebuild 381 BLAKE2B 05a00fd0ca6d8e16bf61fe932f1e9805bac024fbd5bbee7bb4a37e2b3aaa3e394f5d9b8a9d208c127833c25b3de749abf27d849fe2bf0ab22557d565e3ce923f SHA512 b31045a88106d64ddbdd91cb85d06328b99b57eb490aa9f74f9cbf2464e3ed6485ca5e54ebd8146df8aacf0d44ee8f6f1d68cbb7a9e9dd3f2f46d637e2a8404b -MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild deleted file mode 100644 index 8752e78d8fc9..000000000000 --- a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" - -EBO_EAUTORECONF=1 - -inherit emboss-r2 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="sci-biology/meme" - -S="${WORKDIR}/MEME-4.7.650" -PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch deleted file mode 100644 index 56f5814e1efa..000000000000 --- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch +++ /dev/null @@ -1,100 +0,0 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 391989f..d921f25 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ 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}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ 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]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd], -+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] -+ ) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 1600399..9f28162 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml deleted file mode 100644 index d1b9a7602ec2..000000000000 --- a/sci-biology/embassy-meme/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - emboss - - diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 5fd9d2e68b89..cf5e861ca30d 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,4 +1,5 @@ -AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 BLAKE2B 9dfa7b3fb97508e7807b5b3d3ddfa48b1bb78cff3b8e658a0ca786e3c472f997267252c39bde9bbea4311f7b2192c2a0553617a7991e43aca3aa66db289dec41 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249 +AUX embassy-phylipnew-3.69.650-fno-common.patch 16289 BLAKE2B 346f5d704be918503a80ab224e1892953a2d1d6ef642e6ced95fcb1476954e09d983bd0eef1d6afe71d2c4e043a05a99dd92748151e337ac5d3646d91008c2e9 SHA512 0ea1f10865832a44647f0888eabef1df6e5baadace9fda782f171d52eef70fc7d8ef80317d46eaeb029896b8b0b4ca0d845561ae761daf406f7c26e18ebd1341 +AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 39c2d7843ffac8c0a04c70d307d5651f2e53cc386c3a9b1f312d4fd53a9b9ba235a02931c4812a750da8711988e262b1c9a51a7152da20f61cd56c0d21607a89 SHA512 7d46280ffadcbc07e01d09a49a7896539a5c0c271979fcb3e1ffdf385051812adeaabec186c73e2105a710eee2fd340d89bbcbd4ecfa112879fb00cbc58c2dfe DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 -EBUILD embassy-phylipnew-3.69.660.ebuild 361 BLAKE2B 46ace0d20506300a83a423edd19d0305d4e7a072348a7355271dce004e896d92ebd04f2ff342060a5ee2c78f92bd9a6bbccb895eeef462891f78e08d49bcd553 SHA512 3836e21a22a375a4b58fc32b29bdf0481f7bd175b44a131069f6b68ee04d5b507732cc8cc8429afd47f4b26b853c54dd244cd1535a6209708b65989f11d7aa2e +EBUILD embassy-phylipnew-3.69.660.ebuild 409 BLAKE2B 35bac3a33793b140470ef4c627b578317f22efdd7d9c71eeae947f0a6399d94829c5ceeb85d537616811f593b3b54eeda9c1f9bbf0710a20d3eba12891c0f07e SHA512 d088e1121fed9e50066767b58a4d2ea61e5ad5167293cc3780e9bec71f4613d144b985f96d235ab9665a94bff8703a005cdc86916d63cf593941a3e6aeac1165 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild index 3ac088ed6ef9..c5ba6a540bfc 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,4 +14,7 @@ LICENSE+=" free-noncomm" KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/PHYLIPNEW-3.69.650" -PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch + "${FILESDIR}"/${PN}-3.69.650-fno-common.patch +) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch new file mode 100644 index 000000000000..448000547471 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch @@ -0,0 +1,627 @@ +--- a/include/draw.h ++++ b/include/draw.h +@@ -116,19 +116,19 @@ + + + #ifndef X_DISPLAY_MISSING +-Display *display; /* the X display */ ++extern Display *display; /* the X display */ + extern Window mainwin; /* the main display window */ +-int x, y; /* the corner of the window */ +-unsigned int width, height; /* the width and height of the window */ ++extern int x, y; /* the corner of the window */ ++extern unsigned int width, height; /* the width and height of the window */ + #define FONT "-*-new century schoolbook-medium-r-*-*-14-*" +-char *fontrsc; /* the font resource */ +-XFontStruct *fontst; /* the font strcture for the font */ +-XGCValues gcv; /* graphics context values */ +-GC gc1; /* a graphics context */ +-XtAppContext appcontext; +-Widget toplevel; +-int nargc; +-char** nargv; ++extern char *fontrsc; /* the font resource */ ++extern XFontStruct *fontst; /* the font strcture for the font */ ++extern XGCValues gcv; /* graphics context values */ ++extern GC gc1; /* a graphics context */ ++extern XtAppContext appcontext; ++extern Widget toplevel; ++extern int nargc; ++extern char** nargv; + extern String res[16]; + + #define DEFGEOMETRY "600x400+20+50" +--- a/include/phylip.h ++++ b/include/phylip.h +@@ -349,7 +349,8 @@ + extern AjPFile embossancfile; + extern AjPFile embossmixfile; + extern AjPFile embossfactfile; +-extern long spp, words, bits; ++extern AjPPhyloState* phylostates; ++extern long spp, words, bits, outgrno; + extern boolean ibmpc, ansi, tranvsp; + extern naym *nayme; /* names of species */ + +--- a/src/clique.c ++++ b/src/clique.c +@@ -9,7 +9,6 @@ + + #define FormWide 80 /* width of outfile page */ + +-AjPPhyloState* phylostates; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -72,10 +71,8 @@ + Char infilename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long ActualChars, Cliqmin, outgrno, ++long ActualChars, Cliqmin, + col, ith, msets, setsz; + boolean ancvar, Clmin, Factors, outgropt, trout, weights, noroot, justwts, + printcomp, progress, treeprint, mulsets, firstset; +--- a/src/cons.c ++++ b/src/cons.c +@@ -6,7 +6,7 @@ + Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; + node *root; + +-long numopts, outgrno, col, setsz; ++long numopts, col, setsz; + long maxgrp; /* max. no. of groups in all trees found */ + + boolean trout, firsttree, noroot, outgropt, didreroot, prntsets, +--- a/src/consense.c ++++ b/src/consense.c +@@ -19,8 +19,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + long trees_in; + +--- a/src/contml.c ++++ b/src/contml.c +@@ -69,10 +69,8 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long nonodes2, loci, totalleles, df, outgrno, col, ++long nonodes2, loci, totalleles, df, col, + datasets, ith, njumble, jumb=0; + long inseed, inseed0; + long *alleles, *locus, *weight; +--- a/src/contrast.c ++++ b/src/contrast.c +@@ -40,7 +40,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + + +--- a/src/discboot.c ++++ b/src/discboot.c +@@ -56,7 +56,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/disc.c ++++ b/src/disc.c +@@ -1,7 +1,6 @@ + #include "phylip.h" + #include "disc.h" + +-AjPPhyloState* phylostates; + + /* version 3.6. (c) Copyright 1993-2002 by the University of Washington. + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. +--- a/src/discrete.c ++++ b/src/discrete.c +@@ -6,7 +6,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff; + steptr weight, category, alias, location, ally; + sequence y, convtab; +--- a/src/dnacomp.c ++++ b/src/dnacomp.c +@@ -53,8 +53,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root, *p; + long chars, col, ith, njumble, jumb, msets, numtrees; +--- a/src/dnadist.c ++++ b/src/dnadist.c +@@ -27,7 +27,6 @@ + + Char infilename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; +-AjPFile embossoutfile; + + long sites, categs, weightsum, datasets, ith, rcategs; + boolean freqsfrom, jukes, kimura, logdet, gama, invar, similarity, lower, f84, +--- a/src/dnainvar.c ++++ b/src/dnainvar.c +@@ -51,7 +51,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, msets, ith; + boolean weights, progress, prntpat, printinv, mulsets, firstset, justwts; +--- a/src/dnaml.c ++++ b/src/dnaml.c +@@ -93,12 +93,10 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, datasets, ith, njumble, jumb; +-long parens, outgrno; ++long parens; + boolean freqsfrom, global, jumble, weights, trout, usertree, + ctgry, rctgry, auto_, hypstate, ttr, progress, mulsets, justwts, + firstset, improve, smoothit, polishing, lngths, gama, invar,inserting=false; +--- a/src/dnamlk.c ++++ b/src/dnamlk.c +@@ -119,8 +119,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + double *rrate; + long sites, weightsum, categs, datasets, ith, njumble, jumb, numtrees, shimotrees; + /* sites = number of sites in actual sequences +--- a/src/dnamove.c ++++ b/src/dnamove.c +@@ -127,7 +127,6 @@ + node *root; + + const char* outtreename; +-AjPFile embossouttree; + + long chars, screenlines, col, treelines, leftedge, topedge, vmargin, + hscroll, vscroll, scrollinc, screenwidth, farthest, whichtree, othertree; +--- a/src/dnapenny.c ++++ b/src/dnapenny.c +@@ -47,8 +47,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + node *root, *p; + long *zeros=NULL; + long chars, howmany, howoften, col, msets, ith; +--- a/src/dollop.c ++++ b/src/dollop.c +@@ -10,7 +10,6 @@ + + #define maxtrees 100 /* maximum number of tied trees stored */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; +@@ -47,8 +46,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + node *root; +--- a/src/dolmove.c ++++ b/src/dolmove.c +@@ -11,7 +11,6 @@ + #define overr 4 + #define which 1 + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -73,10 +72,9 @@ + Char infilename[FNMLNGTH],intreename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, col, screenlines, screenwidth, scrollinc,treelines, ++long col, screenlines, screenwidth, scrollinc,treelines, + leftedge,topedge,vmargin,hscroll,vscroll,farthest; + /* outgrno indicates outgroup */ + boolean weights, thresh, ancvar, questions, dollo, factors, +--- a/src/dolpenny.c ++++ b/src/dolpenny.c +@@ -15,7 +15,6 @@ + typedef double *valptr; + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + +@@ -40,8 +39,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long howmany, howoften, col, msets, ith; +--- a/src/draw.c ++++ b/src/draw.c +@@ -10,6 +10,20 @@ + #include "phylip.h" + #include "draw.h" + ++#ifndef X_DISPLAY_MISSING ++Display *display; ++int x, y; ++unsigned int width, height; ++char *fontrsc; ++XFontStruct *fontst; ++XGCValues gcv; ++GC gc1; ++XtAppContext appcontext; ++Widget toplevel; ++int nargc; ++char** nargv; ++#endif ++ + #ifdef QUICKC + struct videoconfig myscreen; + void setupgraphics(); +--- a/src/factor.c ++++ b/src/factor.c +@@ -54,7 +54,6 @@ + const char* outfactname; + const char* outancname; + AjPFile inputfile; +-AjPFile embossoutfile; + AjPFile embossoutfact; + AjPFile embossoutanc; + +--- a/src/fitch.c ++++ b/src/fitch.c +@@ -60,11 +60,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +-long nonodes2, outgrno, nums, col, datasets, ith, njumble, jumb=0, numtrees; ++long nonodes2, nums, col, datasets, ith, njumble, jumb=0, numtrees; + long inseed; + vector *x; + intvector *reps; +--- a/src/freqboot.c ++++ b/src/freqboot.c +@@ -52,7 +52,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/gendist.c ++++ b/src/gendist.c +@@ -24,7 +24,6 @@ + #endif + + const char* outfilename; +-AjPFile embossoutfile; + + long loci, totalleles, df, datasets, ith; + long nonodes; +--- a/src/kitsch.c ++++ b/src/kitsch.c +@@ -51,8 +51,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +--- a/src/mix.c ++++ b/src/mix.c +@@ -13,7 +13,6 @@ + + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -52,11 +51,9 @@ + Char infilename[FNMLNGTH], intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, msets, ith, njumble, jumb, numtrees; ++long msets, ith, njumble, jumb, numtrees; + /* outgrno indicates outgroup */ + long inseed, inseed0; + boolean jumble, usertree, weights, ancvar, questions, allsokal, +--- a/src/move.c ++++ b/src/move.c +@@ -13,7 +13,6 @@ + #define which 1 + + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -77,10 +76,9 @@ + + char infilename[FNMLNGTH],intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH]; + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, screenlines, col, treelines, leftedge, topedge, ++long screenlines, col, treelines, leftedge, topedge, + vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest; + /* outgrno indicates outgroup */ + boolean weights, outgropt, ancvar, questions, allsokal, +--- a/src/neighbor.c ++++ b/src/neighbor.c +@@ -32,11 +32,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH]; +-long nonodes2, outgrno, col, datasets, ith; ++long nonodes2, col, datasets, ith; + long inseed; + vector *x; + intvector *reps; +--- a/src/pars.c ++++ b/src/pars.c +@@ -9,7 +9,6 @@ + + #define MAXNUMTREES 1000000 /* bigger than number of user trees can be */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; + +--- a/src/penny.c ++++ b/src/penny.c +@@ -12,7 +12,6 @@ + #define often 100 /* how often to notify how many trees examined */ + #define many 1000 /* how many multiples of howoften before stop */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -44,11 +43,9 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, rno, howmany, howoften, col, msets, ith; ++long rno, howmany, howoften, col, msets, ith; + /* outgrno indicates outgroup */ + + boolean weights, ancvar, questions, allsokal, allwagner, +--- a/src/phylip.c ++++ b/src/phylip.c +@@ -46,7 +46,8 @@ + AjPFile embossancfile; + AjPFile embossmixfile; + AjPFile embossfactfile; +-long spp, words, bits; ++AjPPhyloState* phylostates = NULL; ++long spp, words, bits, outgrno; + boolean ibmpc, ansi, tranvsp; + naym *nayme; /* names of species */ + +--- a/src/proml.c ++++ b/src/proml.c +@@ -89,8 +89,6 @@ + Char infilename[100], intreename[100], catfilename[100], weightfilename[100]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, +--- a/src/promlk.c ++++ b/src/promlk.c +@@ -88,8 +88,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH], + catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; +--- a/src/protdist.c ++++ b/src/protdist.c +@@ -79,7 +79,6 @@ + char infilename[100], catfilename[100], weightfilename[100]; + + const char* outfilename; +-AjPFile embossoutfile; + + + /* Local variables for makedists, propagated globally for c version: */ +--- a/src/protpars.c ++++ b/src/protpars.c +@@ -76,8 +76,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long chars, col, msets, ith, njumble, jumb, numtrees; +--- a/src/restboot.c ++++ b/src/restboot.c +@@ -54,7 +54,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/restdist.c ++++ b/src/restdist.c +@@ -13,7 +13,6 @@ + + extern sequence y; + +-AjPPhyloState* phylostates = NULL; + + + #ifndef OLDC +@@ -40,7 +39,6 @@ + Char infilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, weightsum, datasets, ith; + boolean restsites, neili, gama, weights, lower, +--- a/src/restml.c ++++ b/src/restml.c +@@ -17,7 +17,6 @@ + + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees; +-AjPPhyloState* phylostates = NULL; + + #ifndef OLDC + /* function prototypes */ +@@ -101,8 +100,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + ajint numwts; +--- a/src/retree.c ++++ b/src/retree.c +@@ -123,7 +123,7 @@ + + node *root, *garbage; + +-long nonodes, outgrno, screenwidth, vscreenwidth, ++long nonodes, screenwidth, vscreenwidth, + screenlines, col, treenumber, leftedge, topedge, treelines, + hscroll, vscroll, scrollinc, whichtree, othertree, + numtrees, treesread; +@@ -145,7 +145,6 @@ + char intreename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + boolean subtree, written, readnext; + node *nuroot; +--- a/src/seqbootall.c ++++ b/src/seqbootall.c +@@ -109,7 +109,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seqboot.c ++++ b/src/seqboot.c +@@ -92,7 +92,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seq.c ++++ b/src/seq.c +@@ -7,7 +7,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp; + steptr weight, category, alias, location, ally; + sequence y; +--- a/src/treedist.c ++++ b/src/treedist.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + +--- a/src/treedistpair.c ++++ b/src/treedistpair.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch index 1cba944094a2..95951e632188 100644 --- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 7 ++----- - 3 files changed, 10 insertions(+), 48 deletions(-) - -diff --git a/configure.ac b/configure.ac -index e5bfaf1..09ed517 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index e5bfaf1..09ed517 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL +@@ -781,21 +754,6 @@ @@ -63,7 +56,7 @@ index e5bfaf1..09ed517 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -918,6 +876,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index e5bfaf1..09ed517 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 1883ce9..fb1787f 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ +@@ -16,10 +16,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -102,10 +91,21 @@ index 1883ce9..fb1787f 100644 endif if ISSHARED -@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +31,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -119,6 +116,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest index 2221d6ef0191..389c55c2b131 100644 --- a/sci-biology/gmap/Manifest +++ b/sci-biology/gmap/Manifest @@ -1,3 +1,4 @@ -DIST gmap-gsnap-2015-12-31.v5.tar.gz 4169874 BLAKE2B bbbf53b72b5b7f97ba0eb05db7daa3d1f8a9330f32b96c2460a904a9f9f22078093f6fa585a12d4275e0943145ee78ef99348de4f19349dfa4e81d5f65572e1c SHA512 d42623c60c298d9d3009893432f3eef8cb764bf7cf26b42e6a95b27a468fffab20c8307597c4c8e1afdd61f35652246568c3162137ce59fc4850aaab1062bb48 -EBUILD gmap-2015.12.31.5.ebuild 573 BLAKE2B 0f419e1978d475ea2cc509667d0bf5c389761a42439c8778309217a8b3bcb47215344531784b576d5dba5f0c972cf51a6cafc624f0a0ea3a899387b7a507200b SHA512 8a07e7de0c5d57a2fdc4b7e9da261f469722482be4acdaebcdd76b67d26440ad04cf93ce51a98e908a19ccb6d98bc2725103f9cac7cfcf254812d6499ce8aa70 +AUX gmap-2020.10.27-fno-common.patch 483 BLAKE2B 61055eccbfddd694128288594056d880beaab5f8cf61774c7f745a948fff15ff7e5261c333a0f26152e6f23d8546958e497b7975c9d8150b5279076be05dd4b0 SHA512 ea3de0c56db2c4683cad8471e5f772670288d003e7be8404b8c7528af5d4624c40f390c77b35c3f435ce8459e629783b1d26e8a76f2a479aed3c22feaa78a1a0 +DIST gmap-gsnap-2020-10-27.tar.gz 4480720 BLAKE2B 9f8e8bfab19c079111d42ec466dd145385d35e3fde0a809e46776ed1b62b599664f12618803ea4475b6961a053423a8794d0b77eb0b308bdfa927b5bcaa7d49c SHA512 22e59adf404f5ef524b3cd472fb3124d03c8c55aa7946b9dc3901f5070339dc765f8f1ecc7e394b69a14bf80923f7a9db8d545e45328a346996b3288115a535b +EBUILD gmap-2020.10.27.ebuild 479 BLAKE2B f3363283af3980dd1d95f33d66ea0bbe54780e9d4ff0a1b0c601d545592086a27d4af2c446b500a43a20887bb0df9632e6716fccb3e925e786b007b2ddbe5302 SHA512 7db5938e76273af4063b2c84c292ad657f50d40ccff35fe391217fefcc358882d86dbc5db1fee448b7e36b0ca5a3c6aae438691838df61274df6682d1c473671 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch new file mode 100644 index 000000000000..cc225a78c26e --- /dev/null +++ b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch @@ -0,0 +1,22 @@ +--- a/src/dynprog_end.c ++++ b/src/dynprog_end.c +@@ -109,7 +109,7 @@ + static Trieoffset_T *trieoffsets_max; + static Triecontent_T *triecontents_max; + +-bool homopolymerp; ++static bool homopolymerp; + + void + Dynprog_end_setup (Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in, +--- a/src/dynprog_single.c ++++ b/src/dynprog_single.c +@@ -91,7 +91,7 @@ + + #define T Dynprog_T + +-bool homopolymerp; ++static bool homopolymerp; + + void + Dynprog_single_setup (bool homopolymerp_in) { diff --git a/sci-biology/gmap/gmap-2015.12.31.5.ebuild b/sci-biology/gmap/gmap-2015.12.31.5.ebuild deleted file mode 100644 index 82ae6f3f2748..000000000000 --- a/sci-biology/gmap/gmap-2015.12.31.5.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit versionator - -MY_BASE_PV="$(replace_all_version_separators '-' $(get_version_component_range 1-3))" -MY_PV="${MY_BASE_PV}.v$(get_version_component_range 4)" - -DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" -HOMEPAGE="http://research-pub.gene.com/gmap/" -SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" - -LICENSE="gmap" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -S="${WORKDIR}/gmap-${MY_BASE_PV}" diff --git a/sci-biology/gmap/gmap-2020.10.27.ebuild b/sci-biology/gmap/gmap-2020.10.27.ebuild new file mode 100644 index 000000000000..a90f0f631068 --- /dev/null +++ b/sci-biology/gmap/gmap-2020.10.27.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +MY_PV="$(ver_rs 1- '-')" + +DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" +HOMEPAGE="http://research-pub.gene.com/gmap/" +SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" + +LICENSE="gmap" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/gmap-${MY_PV}" +PATCHES=( "${FILESDIR}"/${PN}-2020.10.27-fno-common.patch ) diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest index bb94011e3eae..6b6322158a4d 100644 --- a/sci-biology/lagan/Manifest +++ b/sci-biology/lagan/Manifest @@ -1,7 +1,11 @@ -AUX lagan-2.0-fix-c++14.patch 13525 BLAKE2B 79037fa65301393f3a007adb424f4a88f72f46ad0cf7c310a07f14b64437fb8fd3dc6da90df5c79e468b424a895797cf01e5b30413435a18ea933d912eb0428e SHA512 f62b523cf9692a1394276ac674ccf7ce9a0070c646c95d1f20b8e0ace61afffd04aae3a098511bb106ab62089e70bebfae6ba25aaffcccbbe7f8397a30c2900a -AUX lagan-2.0-flags.patch 5848 BLAKE2B 41394e65d15be217dea753a9641ee72833ff87f5101fa19ba009f4ca4b97d8fe22594d041105ba03ddb53ad83f635fec79e9125f539eff3cd1cbcdc186d3023e SHA512 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fc255585fc53c66b0a2f4e46788a59f8fdfae67b5f9ca4f4b0ac9224a7a915a387d991cb20315aa18a42df82ffa2b832270f0919f9939faf3b979d026e562c81 +AUX lagan-2.0-qa-implicit-declarations.patch 1396 BLAKE2B 556a43acf76e20a8484fd6ab5d0682b4b29206568b657b8daf09f79577890afd8a594b3897fc2322fffb5e2810a018638af0488c872e9d0794cb685a55b91e79 SHA512 4275aacf1dfa7d712a14ea5d8eafe11045c3b47a02c92915703d095af7b00f2206687eec568d14bfd00718f6b2430bd38cf70ac86cc5d550870d19f5fe6c6d97 DIST lagan20.tar.gz 589115 BLAKE2B 8aaee40b767d7c1828760449e3bf2718210ad345447524ec2c391eb9f2856023f9258618d3d2625b15c42af814615870082bff6320ba0372dff79221798d2618 SHA512 f77217ab534df33834a725eb6e1b716f7bbffa98768a42c2294a6ab62404192e560bb05ffd41e4cdccb5b96ef9efceb8ecdc06472bbc6a301e1d11572ba29b98 -EBUILD lagan-2.0-r3.ebuild 1659 BLAKE2B 0ee31ba110a6238ac9218fc3d59347c9ee97fa11ce097c0a1f5e53c45fefa74ed83e35a1314e2f7fd57fbb3bdb64863109400af32f39f6dba13c273d722ded99 SHA512 b5efe429851ae0a3676a6e63017ebabdcae169667d091b2e69c0c2daa401f34e0ff3b789f8bacd78376befc466bb20de8f0d80bae63c332a6c412f01794f457b +EBUILD lagan-2.0-r4.ebuild 1493 BLAKE2B 81a03c4ab005e5190a2275fa160b86fb16bfb3d8ef1dc794363df692cce7eb8389974af99acbaa5677903db2d75e02e63920cae712abcd7aa421fe7326b8afda SHA512 b9b8e5e12a9ea1276f38806f933cbe7e73b63782510f4e66336ab0a5e1ceeb634d46b81eecf953421d5eaf7e1ce42e130df40b66e6137f0aa8af68155e36363f MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch new file mode 100644 index 000000000000..2c9d88111aee --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch @@ -0,0 +1,258 @@ +--- a/src/fchaos.c ++++ b/src/fchaos.c +@@ -985,7 +985,7 @@ + SLremove(mylist, tbf->mysles[i]); + } + +-inline int CHmatchscore(unsigned char a, unsigned char b) { ++static inline int CHmatchscore(unsigned char a, unsigned char b) { + return substmatrix[a][b]; + /* + if (translated) +--- a/src/multial.c ++++ b/src/multial.c +@@ -59,16 +59,16 @@ + int normf; + int normprev; + +-inline int ismatch(char a, char b) { ++static inline int ismatch(char a, char b) { + return (a == b); + } + +-inline int isGap(align* ali, int seqn, int loc) { ++static inline int isGap(align* ali, int seqn, int loc) { + int i = !((ali->algn[loc] >> seqn) & 1); + return i; + } + +-inline int scoreLocal(int which, align* ali, int loc) { ++static inline int scoreLocal(int which, align* ali, int loc) { + int i, lets = 0; + for (i=0; i < 4; i++) + lets += ali->cnts[i][loc]; +@@ -83,7 +83,7 @@ + return lets+ali->cnts[CNTS_GS][loc] * gapcont; + } + +-inline hll* reverseHLL(hll* tbr) { ++static inline hll* reverseHLL(hll* tbr) { + hll *nn, *prev=0; + while (tbr) { + nn = tbr->next; +@@ -171,7 +171,7 @@ + return res; + } + +-inline void reverse (long long int* a, int length) { ++static inline void reverse (long long int* a, int length) { + long long int lft; + int i; + for (i=0; i < length/2; i++) { +@@ -409,7 +409,7 @@ + */ + } + +-inline int scoreGap(int numgs, int numgc, int numge, int numseq) { ++static inline int scoreGap(int numgs, int numgc, int numge, int numseq) { + return (MIN2(numgc, numseq-numgc) * gapcont) + + (MIN2(numgs, numseq-numgs) * gapstart) + + (MIN2(numge, numseq-numge) * gapend); +@@ -493,7 +493,7 @@ + fclose (file); + } + +-inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) { ++static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) { + return substmatrix[a][b]; + } + +@@ -539,14 +539,14 @@ + // printcache(); + } + +-inline int v (int y){ ++static inline int v (int y){ + if (y >= 0 && y <= MAX_SEQ) return y; + fprintf(stderr, "Got %d in v\n", y); + assert (0); + return 0; + } + +-inline int matchscore (align*a, int ai, align *b, int bi){ ++static inline int matchscore (align*a, int ai, align *b, int bi){ + + return + matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | +@@ -559,30 +559,30 @@ + (v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)]; + } + +-inline int scoreOpp (align *other, int ow, int oppnum){ ++static inline int scoreOpp (align *other, int ow, int oppnum){ + return matchcache[v(other->cnts[0][ow]) | + (v(other->cnts[1][ow]) << 6) | + (v(other->cnts[2][ow]) << 12) | + (v(other->cnts[3][ow]) << 18)]; + } + +-inline int endGap0 (align* a, int ai, align* b, int bi){ ++static inline int endGap0 (align* a, int ai, align* b, int bi){ + return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | + (v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int endGap1 (align* a, int ai, align* b, int bi){ ++static inline int endGap1 (align* a, int ai, align* b, int bi){ + + return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | + (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int endGap2 (align* a, int ai, align* b, int bi){ ++static inline int endGap2 (align* a, int ai, align* b, int bi){ + return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | + (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) { ++static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) { + return gapcache[(v(other->cnts[CNTS_GS][ow])) | + (v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) | + (v(other->cnts[CNTS_GE][ow]) << 12) | +@@ -590,7 +590,7 @@ + sopp[ow]; + } + +-inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) { ++static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) { + int alopen, pen, sav, i; + + alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w]; +--- a/src/order.c ++++ b/src/order.c +@@ -454,11 +454,11 @@ + } + + +-inline int ismatch(char a, char b) { ++static inline int ismatch(char a, char b) { + return a == b; + } + +-inline int matchscore (unsigned char a, unsigned char b) { ++static inline int matchscore (unsigned char a, unsigned char b) { + return substmatrix[a][b]; + /* + +--- a/src/utils/cstat.c ++++ b/src/utils/cstat.c +@@ -121,7 +121,7 @@ + return res; + } + +-inline int getScore (align* a, int i){ ++static inline int getScore (align* a, int i){ + return + ((a->cnts[0][i] * (a->cnts[0][i] - 1)) + + (a->cnts[1][i] * (a->cnts[1][i] - 1)) + +--- a/src/utils/getbounds.c ++++ b/src/utils/getbounds.c +@@ -6,8 +6,8 @@ + + #define EXPAND 2 + +-inline int max (int a, int b){ if (a > b) return a; return b; } +-inline int min (int a, int b){ if (a < b) return a; return b; } ++static inline int max (int a, int b){ if (a > b) return a; return b; } ++static inline int min (int a, int b){ if (a < b) return a; return b; } + + int getLength (char *filename){ + FILE *file; +--- a/src/utils/scorealign.c ++++ b/src/utils/scorealign.c +@@ -18,17 +18,17 @@ + int matchscore[256][256]; + int gapopen = -1500, gapcont = -50; + +-inline int min (int a, int b){ ++static inline int min (int a, int b){ + if (a < b) return a; + return b; + } + +-inline int max (int a, int b){ ++static inline int max (int a, int b){ + if (a > b) return a; + return b; + } + +-inline int scoreMatch (char c, char d){ ++static inline int scoreMatch (char c, char d){ + if (c == '-' && d == '-') return 0; + if (c == '-' || d == '-') return gapcont; + return matchscore[(unsigned char) c][(unsigned char) d]; +@@ -235,7 +235,7 @@ + } + } + +-inline int issymbol (char ch){ ++static inline int issymbol (char ch){ + return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-'; + } + +--- a/src/utils/scorecontigs.c ++++ b/src/utils/scorecontigs.c +@@ -133,7 +133,7 @@ + return res; + } + +-inline int getstate (char c, char d){ ++static inline int getstate (char c, char d){ + if (c == '-' || d == '-') return 2; + if (c == 'N' || d == 'N') return 3; + return c == d; +@@ -235,7 +235,7 @@ + return r; + } + +-inline int getdata (rangelist **ranges, int *offs, int j, int i){ ++static inline int getdata (rangelist **ranges, int *offs, int j, int i){ + i -= offs[j]; + if (i >= 0 && i < ranges[j]->seqlen) + return ranges[j]->score[i]; +@@ -243,14 +243,14 @@ + } + + +-inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){ ++static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){ + int k; + for (k = 0; k < numContigs; k++) + if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0; + return 1; + } + +-inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){ ++static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){ + int i; + + for (i = 0; i < numContigs; i++) +@@ -258,7 +258,7 @@ + return 1; + } + +-inline void print (int start, int end, int *score, int numContigs){ ++static inline void print (int start, int end, int *score, int numContigs){ + int j; + + printf ("(%7d %7d)", start, end); +@@ -303,7 +303,7 @@ + free (pattern); + } + +-inline double scoregap (int gaplen){ ++static inline double scoregap (int gaplen){ + if (gaplen == 0) return 0; + //return (gaplen - 1) * -1 - 50; + return (log (gaplen) / log (10) + 1) * scoreGapOpen; diff --git a/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch new file mode 100644 index 000000000000..945120b1fc47 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch @@ -0,0 +1,49 @@ +Author: Steffen Moeller +Last-Update: 2018-09-07 15:08:19 +0200 +Description: Fix build issue + +Index: lagan/src/glocal/rightinfluence.cpp +=================================================================== +--- lagan.orig/src/glocal/rightinfluence.cpp ++++ lagan/src/glocal/rightinfluence.cpp +@@ -1,6 +1,6 @@ + #include + +-Fragment origin, end; ++static Fragment originFrag, endFrag; + + // Sets the first default owner of the whole region + void initRI(RI *RightInfluence, long long int scoreIndex) { +@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon + } + + // will lose to anyone +- origin.seq1End = 0; origin.seq2End = 0; +- origin.seq1Start = 0; origin.seq2Start = 0; ++ originFrag.seq1End = 0; originFrag.seq2End = 0; ++ originFrag.seq1Start = 0; originFrag.seq2Start = 0; + + // hack to aid winner selection +- origin.score = -1; +- end.score = -2; +- origin.totalScore = end.totalScore = 0; ++ originFrag.score = -1; ++ endFrag.score = -2; ++ originFrag.totalScore = endFrag.totalScore = 0; + + // will win against anyone +- end.seq1End = 0; end.seq2End = 0; +- end.seq1Start = 0; end.seq2Start = 0; ++ endFrag.seq1End = 0; endFrag.seq2End = 0; ++ endFrag.seq1Start = 0; endFrag.seq2Start = 0; + +- origin.back = NULL; ++ originFrag.back = NULL; + +- RightInfluence->act[-INF] = &origin; +- RightInfluence->act[+INF] = &end; ++ RightInfluence->act[-INF] = &originFrag; ++ RightInfluence->act[+INF] = &endFrag; + } + + diff --git a/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch new file mode 100644 index 000000000000..075753a924c9 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch @@ -0,0 +1,24 @@ +Author: Andreas Tille +LastChanged: Fri, 15 Nov 2013 10:31:20 +0100 +Description: Prevent conflicting getline by simply renaming it + +--- a/src/anchors.c ++++ b/src/anchors.c +@@ -225,7 +225,7 @@ char* rolltonum(char* str) { + return &str[i]; + } + +-int getline(FILE* infile, hll* tt) { ++int anchors_getline(FILE* infile, hll* tt) { + char temp[1024]; + char* help; + int z, h; +@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu + *totnum = 0; + while(!feof(infile)) { + tt = (hll*) malloc(sizeof(hll)); +- while (!feof(infile) && !getline(infile, tt)) ++ while (!feof(infile) && !anchors_getline(infile, tt)) + ; + if (feof(infile)) break; + if (gapfreechunks) { diff --git a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch deleted file mode 100644 index 9865f2756c5a..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch +++ /dev/null @@ -1,473 +0,0 @@ -Fix building with C++14, which errors out due to namespace collisions with std::end -in C++14 mode, due to crappy 'using namespace std' declared everywhere. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594148 - ---- a/src/ancseq.cpp -+++ b/src/ancseq.cpp -@@ -30,7 +30,6 @@ - #include - #include - --using namespace std; - - #include "util.cpp" - #include "faindex.cpp" ---- a/src/ancseqrest.cpp -+++ b/src/ancseqrest.cpp -@@ -31,7 +31,6 @@ - #include - #include - --using namespace std; - - #define fastaRowLength 50 - typedef char* pchar; ---- a/src/cutmfa.cpp -+++ b/src/cutmfa.cpp -@@ -45,7 +45,6 @@ - #include - #include - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/glocal/glocal.cpp -+++ b/src/glocal/glocal.cpp -@@ -7,9 +7,9 @@ - } - - //vectors that would be needed globally --vector fragments; --vectorstartPoints; --vectorendPoints; -+std::vector fragments; -+std::vectorstartPoints; -+std::vectorendPoints; - long long int numFragments; - InterPoint inter; - -@@ -19,7 +19,7 @@ - RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - --vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+std::vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - Name allNames; - ---- a/src/glocal/io.cpp -+++ b/src/glocal/io.cpp -@@ -3,9 +3,9 @@ - #include - #include - --extern vector fragments; --extern vector startPoints; --extern vector endPoints; -+extern std::vector fragments; -+extern std::vector startPoints; -+extern std::vector endPoints; - extern Name allNames; - - bool PointCompare(const Point &f1, const Point &f2) { -@@ -223,8 +223,8 @@ - startPoints.push_back(startPoint); - endPoints.push_back(endPoint); - } -- sort(startPoints.begin(), startPoints.end(), PointCompare); -- sort(endPoints.begin(), endPoints.end(), PointCompare); -+ std::sort(startPoints.begin(), startPoints.end(), PointCompare); -+ std::sort(endPoints.begin(), endPoints.end(), PointCompare); - } - - ---- a/src/glocal/leftinfluence.cpp -+++ b/src/glocal/leftinfluence.cpp -@@ -154,8 +154,8 @@ - - if (second->score == -1) { return TRUE; } - -- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2; -- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; -+ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2; -+ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; - - if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) { - dummy.nameIter = first->nameIter; -@@ -444,7 +444,7 @@ - temp.seq1 = col - diag; - temp.seq2 = col; - -- pair pairp(temp, LeftInfluence); -+ std::pair pairp(temp, LeftInfluence); - tempinter = inter.insert(pairp); - - colInter->second = tempinter; ---- a/src/glocal/leftinfluence.h -+++ b/src/glocal/leftinfluence.h -@@ -39,15 +39,15 @@ - - - --typedef list Owner; --typedef map CBound; -+typedef std::list Owner; -+typedef std::map CBound; - --typedef multimap InterPoint; -+typedef std::multimap InterPoint; - --typedef map CInter; --typedef map DBound; -+typedef std::map CInter; -+typedef std::map DBound; - --typedef map DInter; -+typedef std::map DInter; - - - ---- a/src/glocal/rightinfluence.h -+++ b/src/glocal/rightinfluence.h -@@ -17,7 +17,7 @@ - }; - - --typedef map Active; -+typedef std::map Active; - - typedef struct RI { - //List of active regions ---- a/src/glocal/score.cpp -+++ b/src/glocal/score.cpp -@@ -4,7 +4,7 @@ - #include - #include - --extern vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+extern std::vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - - float Score::getScore(Fragment *up, Fragment * down) { -@@ -36,7 +36,7 @@ - - - void initScoreFunctionPointers(char * scoreFileName) { -- ifstream SFP; -+ std::ifstream SFP; - char line[255]; - - SFP.open(scoreFileName); ---- a/src/glocal/structs.h -+++ b/src/glocal/structs.h -@@ -12,7 +12,6 @@ - #include - #include - --using namespace std; - - #define RIGHT 0 - #define LEFT 1 -@@ -49,7 +48,7 @@ - }; - - --typedef map Name; -+typedef std::map Name; - - - typedef struct Fragment { ---- a/src/lagan2mfa.cpp -+++ b/src/lagan2mfa.cpp -@@ -6,7 +6,6 @@ - #include - #include - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/makecons.cpp -+++ b/src/makecons.cpp -@@ -18,7 +18,6 @@ - #include - #include - --using namespace std; - - #define fastaRowLength 50 - #define bufSize 2000 ---- a/src/utils/Glue.cpp -+++ b/src/utils/Glue.cpp -@@ -170,7 +170,7 @@ - } - - void printCoordinates (int seq, int begin, int end){ -- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; -+ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; - } - - int printRegion (int begin, int end){ -@@ -183,7 +183,7 @@ - score += rescoreRegion (seqs[i], seqs[j], begin, end); - } - } -- cout << score << endl; -+ std::cout << score << std::endl; - return score; - } - -@@ -223,7 +223,7 @@ - } - } - -- cout << "= score=" << score << endl; -+ std::cout << "= score=" << score << std::endl; - } - - int countLets (SafeVector &data){ -@@ -355,7 +355,7 @@ - FILE* outfile; - - if (argc < 2 || argc > 3){ -- cerr << "Usage: Glue align.mfa \n" << endl; -+ std::cerr << "Usage: Glue align.mfa \n" << std::endl; - exit (1); - } - -@@ -375,7 +375,7 @@ - SafeVector merged1label, merged2label; - int begin1 = 1, end1 = 1; - -- ifstream data (argv[1]); -+ std::ifstream data (argv[1]); - int alignNum = 0; - strand.push_back ('?'); // nothing for alignNum 0 - -@@ -452,7 +452,7 @@ - SafeVector temp1 (begin1 - 1, 'N'); - SafeVector temp2 (begin1 - 1, '-'); - -- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++) -+ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++) - temp2[i] = 'N'; - - merged1 = merge (temp1, merged1); -@@ -471,12 +471,12 @@ - if (isalpha(merged2[j])) pos2++; - - if (merged1label[j] == i){ -- min1 = min (min1, pos1); -- max1 = max (max1, pos1); -+ min1 = std::min (min1, pos1); -+ max1 = std::max (max1, pos1); - } - if (merged2label[j] == i){ -- min2 = min (min2, pos2); -- max2 = max (max2, pos2); -+ min2 = std::min (min2, pos2); -+ max2 = std::max (max2, pos2); - } - } - -@@ -489,6 +489,6 @@ - fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2); - } - -- printMFA (cout, merged1, string ("first"), 60); -- printMFA (cout, merged2, string ("second"), 60); -+ printMFA (std::cout, merged1, std::string ("first"), 60); -+ printMFA (std::cout, merged2, std::string ("second"), 60); - } ---- a/src/utils/MultiSequence.h -+++ b/src/utils/MultiSequence.h -@@ -12,7 +12,6 @@ - #include "Sequence.h" - #include "SafeVector.h" - --using namespace std; - - class MultiSequence { - private: -@@ -54,10 +53,10 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (const string& filename){ -+ void addRawFromMFA (const std::string& filename){ - - // open up file for reading -- ifstream infile (filename.c_str()); -+ std::ifstream infile (filename.c_str()); - - // check for error - assert (!infile.fail()); -@@ -75,7 +74,7 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (ifstream &infile){ -+ void addRawFromMFA (std::ifstream &infile){ - - // check for error - assert (!infile.fail()); -@@ -89,7 +88,7 @@ - } - - // Writes sequences to outfile in XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - for (int i = 0; i < (int) sequences.size(); ++i){ - sequences[i].writeToXMFA (outfile, numColumns); - } ---- a/src/utils/Output.h -+++ b/src/utils/Output.h -@@ -2,18 +2,18 @@ - #define OUTPUT_H - - // print reversed string in MFA format --void printMFA (ostream &outfile, SafeVector &data, string comment, int numColumns){ -+void printMFA (std::ostream &outfile, SafeVector &data, std::string comment, int numColumns){ - - int charsWritten = 0; - -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - for (int i = 0; i < (int) data.size(); i++){ - outfile << data[i]; - charsWritten++; -- if (charsWritten % numColumns == 0) outfile << endl; -+ if (charsWritten % numColumns == 0) outfile << std::endl; - } - -- if (charsWritten % numColumns != 0) outfile << endl; -+ if (charsWritten % numColumns != 0) outfile << std::endl; - } - - ---- a/src/utils/SafeVector.h -+++ b/src/utils/SafeVector.h -@@ -10,7 +10,6 @@ - #include - #include - --using namespace std; - - // class derived from the STL std::vector - template -@@ -19,9 +18,9 @@ - - // miscellaneous constructors - SafeVector () {} -- SafeVector (size_t size) : vector(size) {} -- SafeVector (size_t size, const TYPE &value) : vector(size, value) {} -- SafeVector (const SafeVector &source) : vector(source) {} -+ SafeVector (size_t size) : std::vector(size) {} -+ SafeVector (size_t size, const TYPE &value) : std::vector(size, value) {} -+ SafeVector (const SafeVector &source) : std::vector(source) {} - - #ifdef ENABLE_CHECKS - ---- a/src/utils/Sequence.h -+++ b/src/utils/Sequence.h -@@ -8,15 +8,14 @@ - #include - #include "SafeVector.h" - --using namespace std; - - class Sequence { - - private: - - // Read header of MFA/XMFA file. -- bool readHeader (ifstream &infile, bool &isXMFA){ -- string header; -+ bool readHeader (std::ifstream &infile, bool &isXMFA){ -+ std::string header; - - while (true){ - -@@ -24,7 +23,7 @@ - if (infile.fail() || infile.eof()) return false; - - // get new header line -- getline (infile, header); -+ std::getline (infile, header); - - // check that header line is not empty - if (header.length() != 0) break; -@@ -64,7 +63,7 @@ - int startCoord; // sequence position of first character - int endCoord; // sequence position of last character - char direction; // + or - -- string comment; // comments -+ std::string comment; // comments - - public: - -@@ -77,7 +76,7 @@ - } - - // Constructor. Reads in a sequence from the input file. -- Sequence (ifstream &infile){ -+ Sequence (std::ifstream &infile){ - - bool isXMFA = true; - -@@ -147,7 +146,7 @@ - } - - // Constructor. Gets sequence from array data. -- Sequence (SafeVector data, string comment) : data(data), comment(comment) { -+ Sequence (SafeVector data, std::string comment) : data(data), comment(comment) { - length = data.size() - 1; - id = 0; - startCoord = 1; -@@ -165,7 +164,7 @@ - return temp; - } - -- const string getComment () const { -+ const std::string getComment () const { - return comment; - } - -@@ -197,9 +196,9 @@ - const int getEndCoord () const { assert (isValid); return endCoord; } - - // Print XMFA header only. -- void writeXMFAHeader (ostream &outfile) const { -+ void writeXMFAHeader (std::ostream &outfile) const { - assert (isValid); -- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; -+ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl; - } - - // Return sequence ID. -@@ -209,20 +208,20 @@ - void setID (int id) { assert (isValid); this->id = id; } - - // Writes sequence to XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - - assert (isValid); - - // print XMFA header -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - // outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; - - // print character data - for (int i = 1; i <= length; ++i){ - outfile << data[i]; -- if (i % numColumns == 0) outfile << endl; -+ if (i % numColumns == 0) outfile << std::endl; - } -- if (length % numColumns != 0) outfile << endl; -+ if (length % numColumns != 0) outfile << std::endl; - } - }; - diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch deleted file mode 100644 index e324ef64c4c6..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-flags.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff --git a/Makefile b/Makefile -index fbbbe79..a1d449b 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,5 +1,5 @@ - all: -- (cd src; $(MAKE)) -+ $(MAKE) -C src - clean: - rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay - (cd src; $(MAKE) clean) -diff --git a/src/Makefile b/src/Makefile -index 7f6b6fd..dd6309b 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W - TRGT_DIR = .. - - all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay -- (cd glocal; $(MAKE)) -+ $(MAKE) -C glocal - clean: - rm -f *.o *~ utils/*~ mlagan.purify core - (cd glocal; $(MAKE) clean) - ../anchors: anchors.c skiplist.c -- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c - ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c -- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG - ../order: order.c diagmatrix.c filebuffer.c -- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c - ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c -- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG - ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c -- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG - ../utils/bin2mf: utils/bin2mf.c -- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c - ../utils/bin2bl: utils/bin2bl.c -- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c - ../utils/cextract: utils/cextract.c -- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c - ../utils/cstat: utils/cstat.c -- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c - ../utils/contigorder: utils/contigorder.c -- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c - ../utils/getbounds: utils/getbounds.c -- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c - ../utils/getcontigpos: utils/getcontigpos.c -- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c - ../utils/getlength: utils/getlength.c -- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c - ../utils/getoverlap: utils/getoverlap.c -- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c - ../utils/rc: utils/rc.c -- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c - ../utils/seqmerge: utils/seqmerge.c -- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c - ../utils/scorealign: utils/scorealign.c -- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm - ../utils/scorecontigs: utils/scorecontigs.c -- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm - ../utils/fa2xfa: utils/fa2xfa.c -- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c - ../utils/overlay: utils/overlay.c -- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c - ../utils/Glue: utils/Glue.cpp -- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp - ../utils/dotplot: utils/dotplot.cpp -- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp -diff --git a/src/glocal/Makefile b/src/glocal/Makefile -index ce1421a..b82507f 100755 ---- a/src/glocal/Makefile -+++ b/src/glocal/Makefile -@@ -10,10 +10,10 @@ TRGT = glocal - OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o - - .cpp.o: -- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp -+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp - - $(TRGT): $(OBJECTS) -- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) -+ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) - - clean : - rm -f *.o ./*~ *~ core diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch new file mode 100644 index 000000000000..bd9824cf2ed0 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch @@ -0,0 +1,27 @@ +Description: Add patch to build with GCC-10 +Bug-Debian: https://bugs.debian.org/957415 +Author: Nilesh Patra +Date: Fri Apr 17 21:13:21 2020 +0530 + +--- a/src/fchaos.c ++++ b/src/fchaos.c +@@ -29,7 +29,7 @@ + int offset; + } match; + +-extern int indeces[256]; ++int indeces[256]; + + + void remElem(LList* tbf, int i); +--- a/src/thrtrie.h ++++ b/src/thrtrie.h +@@ -2,7 +2,7 @@ + #define MAX_DEGEN 2 + + +-int indeces[256]; ++extern int indeces[256]; + + typedef struct PrevHits { + int* inds1; diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch new file mode 100644 index 000000000000..3d7ed780445f --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch @@ -0,0 +1,25 @@ +Author: Andreas Tille +LastChanged: Fri, 15 Nov 2013 10:31:20 +0100 +Description: Fix some includes to build using gcc-4.8 + +--- a/src/utils/Glue.cpp ++++ b/src/utils/Glue.cpp +@@ -6,6 +6,7 @@ + #include + #include + #include ++#include + + #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" + #define MAX_LINE_LENGTH 1024 +--- a/src/glocal/score.cpp ++++ b/src/glocal/score.cpp +@@ -2,7 +2,7 @@ + #include + #include + #include +-#include ++#include + + extern vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-9.patch b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch new file mode 100644 index 000000000000..6ea30e57a854 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch @@ -0,0 +1,25 @@ +# Two patches to bring lagan up to speed with gcc-9 +Index: lagan/src/fchaos.c +=================================================================== +--- lagan.orig/src/fchaos.c ++++ lagan/src/fchaos.c +@@ -430,7 +430,7 @@ int chain(LList* second, int off2, LList + int tc =0; + int wc = 0; + +-inline void findPrev(LList* curr, int position, int offset, float baseval) { ++void findPrev(LList* curr, int position, int offset, float baseval) { + int j,k; + LList* temp; + sle* iterator; +Index: lagan/src/filebuffer.c +=================================================================== +--- lagan.orig/src/filebuffer.c ++++ lagan/src/filebuffer.c +@@ -1,5 +1,6 @@ + #include "filebuffer.h" + #include ++#include + #include + #include + #include diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch deleted file mode 100644 index a4b1d6808e2f..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp ---- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000 -+++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000 -@@ -2,7 +2,7 @@ - #include - #include - #include --#include -+#include - - extern vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - -diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp ---- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000 -+++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000 -@@ -1,6 +1,7 @@ - #include "MultiSequence.h" - #include "SafeVector.h" - #include "Output.h" -+#include - #include - #include - #include diff --git a/sci-biology/lagan/files/lagan-2.0-makefile.patch b/sci-biology/lagan/files/lagan-2.0-makefile.patch new file mode 100644 index 000000000000..1bef6721ab9b --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-makefile.patch @@ -0,0 +1,120 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,8 @@ + all: +- (cd src; $(MAKE)) ++ $(MAKE) -C src + clean: + rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay +- (cd src; $(MAKE) clean) ++ $(MAKE) -C src clean ++ ++check: all ++ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" +--- a/src/glocal/Makefile ++++ b/src/glocal/Makefile +@@ -1,19 +1,13 @@ +-CC = g++ +-OPTFLAGS = +-CFLAGS = $(OPTFLAGS) -O3 +-CLINKER = g++ +-# LIBDIR = -L/usr/local/lib ++CXXFLAGS += -Wno-deprecated ++CPPFLAGS += -I./ ++ + MLIB = -lm +-INCDIR = -I./ + TRGT_DIR = ../.. + TRGT = glocal + OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o + +-.cpp.o: +- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp +- + $(TRGT): $(OBJECTS) +- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) + + clean : + rm -f *.o ./*~ *~ core +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,54 +1,51 @@ +-CC = gcc $(CFLAGS) +-CPP = g++ $(CFLAGS) +-CFLAGS = -O3 # -Wall -W + TRGT_DIR = .. + + all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay +- (cd glocal; $(MAKE)) ++ (cd glocal && $(MAKE)) + clean: + rm -f *.o *~ utils/*~ mlagan.purify core +- (cd glocal; $(MAKE) clean) ++ (cd glocal && $(MAKE) clean) + ../anchors: anchors.c skiplist.c +- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c + ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG + ../order: order.c diagmatrix.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c + ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../utils/bin2mf: utils/bin2mf.c +- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c + ../utils/bin2bl: utils/bin2bl.c +- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c + ../utils/cextract: utils/cextract.c +- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c + ../utils/cstat: utils/cstat.c +- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c + ../utils/contigorder: utils/contigorder.c +- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c + ../utils/getbounds: utils/getbounds.c +- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c + ../utils/getcontigpos: utils/getcontigpos.c +- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c + ../utils/getlength: utils/getlength.c +- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c + ../utils/getoverlap: utils/getoverlap.c +- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c + ../utils/rc: utils/rc.c +- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c + ../utils/seqmerge: utils/seqmerge.c +- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c + ../utils/scorealign: utils/scorealign.c +- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm + ../utils/scorecontigs: utils/scorecontigs.c +- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm + ../utils/fa2xfa: utils/fa2xfa.c +- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c + ../utils/overlay: utils/overlay.c +- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c + ../utils/Glue: utils/Glue.cpp +- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp + ../utils/dotplot: utils/dotplot.cpp +- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp diff --git a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch index 4ba4ce49d770..29db043d5f34 100644 --- a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch +++ b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch @@ -1,69 +1,34 @@ -Fix QA warnings due to implicit declarations: -* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] -* temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? - ---- a/src/filebuffer.c -+++ b/src/filebuffer.c -@@ -3,6 +3,7 @@ - #include - #include - #include -+#include - - #ifdef CHAOS__FLAG - char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*"; --- a/src/mlagan.c +++ b/src/mlagan.c -@@ -934,6 +934,7 @@ - return k; +@@ -46,6 +46,7 @@ + return 1; } +int printXMFAAlign(FILE* outfile, align* myalign); - int main(int argc, char** argv) { - FileBuffer seqfile; + void usage(void) { + printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n", --- a/src/order.c +++ b/src/order.c -@@ -398,6 +398,9 @@ - free(ends); - } +@@ -28,6 +28,8 @@ + + align* makeAlign(dmat* mydm, char* seq1, char* seq2); +int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); +int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); -+ - void doAlign(dmat* mydm, seq* seq1, seq* seq2) { - align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets); - // printf("into printing\n"); + + char* alpha = "ATCGN."; + --- a/src/prolagan.c +++ b/src/prolagan.c -@@ -949,6 +949,7 @@ - return k; +@@ -49,6 +49,7 @@ + return 1; } +int printXMFAAlign(FILE* outfile, align* myalign); - int main(int argc, char** argv) { - FileBuffer seqfile; ---- a/src/utils/contigorder.c -+++ b/src/utils/contigorder.c -@@ -12,7 +12,7 @@ - int dummy, i; - - if (!(file = fopen (filename, "r"))){ -- fprintf (stderr, "contigorder: Error opening file: %s\n"); -+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); - exit (1); - } - -@@ -49,7 +49,7 @@ - } - - if (!(file = fopen (filename, "r"))){ -- fprintf (stderr, "contigorder: Error opening file: %s\n"); -+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); - exit (1); - } - + void usage(void) { + printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n", --- a/src/utils/cstat.c +++ b/src/utils/cstat.c @@ -3,6 +3,7 @@ diff --git a/sci-biology/lagan/lagan-2.0-r3.ebuild b/sci-biology/lagan/lagan-2.0-r3.ebuild deleted file mode 100644 index e326331e09fb..000000000000 --- a/sci-biology/lagan/lagan-2.0-r3.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -MY_P="lagan20" - -DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA" -HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" -SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-lang/perl" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}/${PN}-2.0-flags.patch" - "${FILESDIR}/${PN}-2.0-gcc4.3.patch" - "${FILESDIR}/${PN}-2.0-fix-c++14.patch" - "${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch" -) - -src_prepare() { - sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die - # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h - # where libc getline is erroneously used instead of own getline - sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die - - default -} - -src_compile() { - emake \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - CXXFLAGS="${CXXFLAGS}" \ - CFLAGS="${CFLAGS}" -} - -src_install() { - newbin lagan.pl lagan - newbin slagan.pl slagan - dobin mlagan - rm -f lagan.pl slagan.pl utils/Utils.pm || die - - insinto /usr/$(get_libdir)/${PN}/lib - doins Utils.pm - - exeinto /usr/$(get_libdir)/${PN}/utils - doexe utils/* - - exeinto /usr/$(get_libdir)/${PN} - doexe *.pl anchors chaos glocal order prolagan - - insinto /usr/$(get_libdir)/${PN} - doins *.txt - - dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap - - echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die - doenvd 99${PN} - - dodoc Readmes/README.* -} diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild new file mode 100644 index 000000000000..4582d8f1078e --- /dev/null +++ b/sci-biology/lagan/lagan-2.0-r4.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +MY_P="lagan20" + +DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA" +HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" +SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl" + +S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-conflicting-getline.patch + "${FILESDIR}"/${P}-gcc-4.8.patch + "${FILESDIR}"/${P}-ambiguous-end.patch + "${FILESDIR}"/${P}-gcc-9.patch + "${FILESDIR}"/${P}-gcc-10.patch + "${FILESDIR}"/${P}-C99-static-inline.patch + "${FILESDIR}"/${P}-qa-implicit-declarations.patch +) + +src_prepare() { + default + sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \ + supermap.pl || die +} + +src_configure() { + tc-export CC CXX +} + +src_install() { + newbin lagan.pl lagan + newbin slagan.pl slagan + dobin mlagan + rm lagan.pl slagan.pl utils/Utils.pm || die + + insinto /usr/$(get_libdir)/lagan/lib + doins Utils.pm + + exeinto /usr/$(get_libdir)/lagan/utils + doexe utils/* + + exeinto /usr/$(get_libdir)/lagan + doexe *.pl anchors chaos glocal order prolagan + + insinto /usr/$(get_libdir)/lagan + doins *.txt + + dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap + + newenvd - 99lagan <<- _EOF_ + LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan" + _EOF_ + + dodoc Readmes/README.* +} diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest deleted file mode 100644 index 773a56aca2d6..000000000000 --- a/sci-biology/meme/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -AUX meme-4.11.2_p2-fix-build-system.patch 10447 BLAKE2B 5ca1f4b43247f00b09012f503e0198306db39aa9992e56865d130d40f1530452784bf9edb508ad37d15fe4427fa2d19d4781db35e1f2b1b0257e8214e92734a4 SHA512 85181e114e825081ef52545fef7ab638c91029964eb8be2e1e4042d1d766d5376dbcabc9bd3902f19d162997dd63cb02fea66d231df6bafc0e74981373ea9724 -AUX meme-4.11.2_p2-patch1.patch 13820 BLAKE2B 3d5815bfe966e1d77cdf4491f34f3b3bd8ea674a5510a63d3cec0d0710c29d6d8cb6b1c284f2c8e9259687975644d39afabaf7c3708a3023d3939be4bf3174c1 SHA512 5a5989b5c626dee6aeaa435ce6c444caed6711d62216743d97215abddef95eb92c66544576866fc43c8efb090410aaed425231642dfcd9634b3f3025d5f1981f -AUX meme-4.11.2_p2-patch2.patch 1684 BLAKE2B 7e5e22f90aa8424d26239a44e56c91ffe6709667a57bd73e058f1b9b012e3873ea6c226bfceefd4ab57989c3059f1fd2bf057bbc253620110fe26bb6370f6e7c SHA512 9c9b01196f76e3b02fa40c7a4d20bc77622cc3ac188584a53774be4ad72a889a72a7a57b38dda81fc7f1bb23db20eec50b0778b71caade4ddf65e49407f3ef8a -DIST meme_4.11.2.tar.gz 18004930 BLAKE2B accacc7d2422ff6ea3411ff43ea664c94f5d6ba320e1cfec642a88cb6ea5303b2fe8c99a6c35d865c377560118402ab11f869930fd108f02eeaa06321db21655 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 -EBUILD meme-4.11.2_p2.ebuild 2352 BLAKE2B d5946ace6bebec5fe7714b6db3d13185b7fb1cd07e4f24d1a6c7474556c8ed6a16e95f3ae2a3ace62c5e75ad1e8cf5f2832b6dafc2a3276d47e7a1c43c329b5d SHA512 fa4bd73f96f5f0f05dbbd12d316abe49d0414978cbcdc25bb625c288feb346d979c955316298489d951430faf60354f380ead663d04e5e711789e67d6be52e63 -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch deleted file mode 100644 index b548de5a39a5..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch +++ /dev/null @@ -1,346 +0,0 @@ -Fix and modernise build system -* Remove all *FLAGS setting, just append to the user-supplied ones -* Add --enable-doc and --enable-examples configure flags -* Install documentation and examples in correct directories -* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES -* Install python and perl modules correctly - ---- a/configure.ac -+++ b/configure.ac -@@ -76,61 +76,10 @@ - AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no]) - - # Check for compiler-specific settings --LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` --if test "${GCC}" = "yes"; then -- ac_cc_opt="-O3" -- ac_cc_debug_opt="-O0" -- ac_cc_warn="-Wall -Wno-unused" -- ac_cc_debug="-ggdb" -- # Check for OS X llvm (clang) compiler -- if `gcc --version |grep llvm >/dev/null`; then -- ac_cc_debug="-g" -- fi -- CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --else -- ac_cc_opt="-O" -- ac_cc_debug_opt="" -- ac_cc_warn="" -- ac_cc_debug="-g" -- CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --fi -- --# Set up default libxml2 settings --# check for installed copy of libxml2 --build_libxml2="yes" --if test -n "$XML2_CONFIG"; then -- # Require at least version 2.6 -- required_libxml2_version="2006000" -- LIBXML2_VERSION="`$XML2_CONFIG --version | \ -- awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`" -- if test -n "$LIBXML2_VERSION" && \ -- test "$LIBXML2_VERSION" -ge "$required_libxml2_version"; then -- build_libxml2="no" -- LIBXML2_LIBS="`$XML2_CONFIG --libs`" -- LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`" -- fi --fi --if test -z "$LIBXML2_LIBS"; then -- AC_MSG_WARN([libxml2 library not found]) -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" --fi -- --# Set up default libxslt settings --# check for installed copy of libxslt --build_libxslt="yes" --if test -n "$XSLT_CONFIG"; then -- build_libxslt="no" -- LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt" -- LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`" --fi --if test -z "$LIBXSLT_LIBS"; then -- AC_MSG_WARN([libxslt library not found]) -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" --fi -+AC_PROG_MKDIR_P -+AC_SYS_LARGEFILE -+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}" -+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}" - - # who is installing - USER=`whoami` -@@ -279,6 +227,16 @@ - AM_CONDITIONAL(PARALLEL, test ["$parallel" != no]) - AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) - -+dnl Documentation -+AC_ARG_ENABLE([doc], -+ AS_HELP_STRING([--enable-doc], [Enable installation of documentation])) -+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"]) -+ -+dnl Examples -+AC_ARG_ENABLE([examples], -+ AS_HELP_STRING([--enable-examples], [Enable installation of examples])) -+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"]) -+ - AC_ARG_ENABLE( - webservice, - [ --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation], -@@ -309,24 +267,35 @@ - AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"]) - - # enable building of included libxml2 --AC_ARG_ENABLE( -- build_libxml2, -- [ --enable-build-libxml2 Build included version of libxml2. Default is to use pre-existing locally installed copy.], -- build_libxml2=$enableval; \ -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \ -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , ) --AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes]) -+AC_ARG_ENABLE([build-libxml2], -+ AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxml2" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" -+ LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6]) -+]) -+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"]) -+ - - # enable building of included libxslt --AC_ARG_ENABLE( -- build_libxslt, -- [ --enable-build-libxslt Build included version of libxslt. Default is to use pre-existing locally installed copy.], -- build_libxslt=$enableval; \ -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \ -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \ -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \ -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , ) --AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes]) -+AC_ARG_ENABLE([build-libxslt], -+ AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxslt" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" -+ LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -+ -+ LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -+ LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXSLT], [libxslt]) -+ PKG_CHECK_MODULES([LIBEXSLT], [libexslt]) -+]) -+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"]) - - # set website url - AC_ARG_WITH( -@@ -427,13 +396,13 @@ - [AC_PATH_PROG(PERL, perl)]) - AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] ) - -+AC_ARG_WITH([perl-dir], -+ AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"]) -+AC_SUBST([perlmoddir]) -+ -+ - # set path to Python --AC_ARG_WITH( -- python, -- [ --with-python=NAME Set path to Python. Default is to take from user's PATH.], -- [PYTHON=$withval], -- [AC_PATH_PROG(PYTHON, python)]) --AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] ) -+AM_PATH_PYTHON - - # set path to convert utility - AC_ARG_WITH( -@@ -586,13 +555,15 @@ - Configuration parameters - ======================== - -- Install path: ${prefix} -+ Install path (prefix): ${prefix} - Install UID: ${MEME_USER} - Version: ${VERSION} -- C compiler: ${CC} -- C compiler flags: ${CFLAGS} -- Linker: ${LD} -- Special Libs: ${LIBS} -+ C compiler (CC): ${CC} -+ C compiler flags (CFLAGS): ${CFLAGS} -+ C preproc flags (CPPFLAGS): ${CPPFLAGS} -+ Linker (LD): ${LD} -+ Linker flags (LDFLAGS): ${LDFLAGS} -+ Special Libs (LIBS): ${LIBS} - MPICC ${MPICC} - MPIRUN ${MPIRUN} - MPI_CMD ${MPI_CMD} ---- a/doc/css/Makefile.am -+++ b/doc/css/Makefile.am -@@ -5,7 +5,7 @@ - - EXTRA_DIST = $(NORMAL_FILES) - --if ! WEBSITE --doccssdir = $(prefix)/doc/css -+if ENABLE_DOC -+doccssdir = $(htmldir)/css - doccss_DATA = $(NORMAL_FILES) - endif ---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am -+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am -@@ -7,8 +7,8 @@ - EXAMPLES = \ - prior.dist.txt - --if ! WEBSITE --exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/compute_prior_dist_example_output_files - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/examples/Makefile.am -+++ b/doc/examples/Makefile.am -@@ -22,8 +22,8 @@ - # load the EXAMPLE_OUTPUT_FILES variable - include examples.mk - --if ! WEBSITE --exdir = $(prefix)/doc/examples -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples - nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES) - endif - ---- a/doc/examples/sample_opal_scripts/Makefile.am -+++ b/doc/examples/sample_opal_scripts/Makefile.am -@@ -15,8 +15,8 @@ - MemeClient.pl \ - MemeClient.py - --if ! WEBSITE --exdir = $(prefix)/doc/examples/sample_opal_scripts -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/sample_opal_scripts - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/images/Makefile.am -+++ b/doc/images/Makefile.am -@@ -30,8 +30,8 @@ - - MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES) - --if ! WEBSITE --memeimgdir = $(prefix)/doc/images -+if ENABLE_DOC -+memeimgdir = $(htmldir)/images - memeimg_DATA = $(MEME_IMAGES) - endif - ---- a/doc/js/Makefile.am -+++ b/doc/js/Makefile.am -@@ -41,8 +41,8 @@ - - BUILT_SOURCES = $(BUILT_FILES) - --if ! WEBSITE --docjsdir = $(prefix)/doc/js -+if ENABLE_DOC -+docjsdir = $(htmldir)/js - docjs_DATA = $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES) - endif - ---- a/doc/Makefile.am -+++ b/doc/Makefile.am -@@ -129,8 +129,8 @@ - update-sequence-db.html \ - ismb94.pdf - --if ! WEBSITE --memedocdir = $(prefix)/doc -+if ENABLE_DOC -+memedocdir = $(htmldir) - memedoc_DATA = $(NORMAL_FILES) - endif - ---- a/Makefile.am -+++ b/Makefile.am -@@ -52,7 +52,7 @@ - endif - - dbdir: -- mkdir -p $(MEME_DB) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_DB) - - all-local: - if WEBSITE -@@ -64,8 +64,8 @@ - endif - - install-data-local: -- mkdir -p $(MEME_LOGS) -- chmod a+w $(MEME_LOGS) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_LOGS) -+ chmod a+w $(DESTDIR)/$(MEME_LOGS) - - distdir = $(PACKAGE)_$(VERSION) - ---- a/scripts/Makefile.am -+++ b/scripts/Makefile.am -@@ -22,8 +22,8 @@ - -e 's%@WHICHJAVA@%$(JAVA)%' \ - -e 's%@WHICHCONVERT@%$(CONVERT)%' \ - -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \ -- -e 's%@PERLLIBDIR@%$(libdir)/perl%' \ -- -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \ -+ -e 's%@PERLLIBDIR@%$(perlmoddir)%' \ -+ -e 's%@PYTHONLIBDIR@%$(pythondir)%' \ - -e 's%@JAVALIBDIR@%$(libdir)/java%' \ - -e 's%@LAM_BIN@%$(LAMBIN)%' \ - -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \ -@@ -62,7 +62,7 @@ - DiffXML.pm \ - HypergeometricDynProg.pm - --perlmoddir=$(libdir)/perl -+perlmoddir = $(exec_prefix)/@perlmoddir@ - perlmod_SCRIPTS = \ - $(BUILT_PERL_MOD) \ - $(NORMAL_PERL_MOD) -@@ -76,8 +76,7 @@ - hypergeometric.py \ - sequence.py - --pythonlibdir=$(libdir)/python --pythonlib_SCRIPTS = \ -+python_PYTHON = \ - $(BUILT_PYTHON_LIB) \ - $(NORMAL_PYTHON_LIB) - ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -19,7 +19,13 @@ - ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) - ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE) - --SUBDIRS = filters libxml2 libxslt libexslt . parallel -+SUBDIRS = filters . parallel -+if BUILD_LIBXML2 -+SUBDIRS += libxml2 -+endif -+if BUILD_LIBXSLT -+SUBDIRS += libxslt libexslt -+endif - - BUILT_SOURCES = dir.h projrel.h - diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch deleted file mode 100644 index 30a182f8f43a..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch +++ /dev/null @@ -1,383 +0,0 @@ ---- a/doc/alphabet-format.html -+++ b/doc/alphabet-format.html -@@ -233,7 +233,7 @@ - providing a reference on the meaning of the symbols used. If present, the - symbol name must be the second field.

-

The "name" follows the rules of -- quoted text.

-+ quoted text.

- -
color
-
---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -14,8 +14,26 @@ -

Motif-based sequence analysis tools

-
-

MEME Suite Release Notes

-+
-+ MEME version 4.11.2 patch 1 -- June 16, 2016 -+
    -+
  • -+ Bug fixes -+
      -+
    • -+ Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate -+ reading the sequence file. -+
      • -+
    • -+ Modified MEME to fall back to a simple Dirichlet prior when -+ using DNA or a custom alphabet with a prior that requires -+ a prior library, but no prior libray is specified. -+
      • -+
    -+
-+

-

--

- MEME version 4.11.2 -- May 5 2016 -

-
    ---- a/src/fasta-io.c -+++ b/src/fasta-io.c -@@ -14,6 +14,7 @@ - #include "alphabet.h" - #include "fasta-io.h" - #include "io.h" -+#include "seq-reader-from-fasta.h" - #include "prior-reader-from-psp.h" - #include "seq.h" - -@@ -159,61 +160,6 @@ - } - - /**************************************************************************** -- * Read raw sequence until a new sequence is encountered or too many letters -- * are read. The new sequence is appended to the end of the given -- * sequence. -- * -- * Return: Was the sequence read completely? -- ****************************************************************************/ --static BOOLEAN_T read_raw_sequence_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, // Sequence source -- char* name, // Sequence ID (used in error messages). -- ALPH_T* alph, // Alphabet in use -- unsigned int offset, // Current position in raw_sequence. -- unsigned int max_chars, // Maximum chars in raw_sequence. -- char* raw_sequence // Pre-allocated sequence. --) { -- // tlb; change a_char to integer so it will compile on SGI -- int a_char; -- int start_update; -- BOOLEAN_T return_value = TRUE; -- -- // Start at the end of the given sequence. -- assert(offset < max_chars); -- -- DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset); -- return_value = !fasta_reader->get_next_block(fasta_reader, seq_block); -- -- char *seq_buffer = get_sequence_from_data_block(seq_block); -- size_t seq_buffer_size = get_num_read_into_data_block(seq_block); -- int i; -- for (i = 0; i < seq_buffer_size; ++i) { -- a_char = seq_buffer[i]; -- // Skip non-alphabetic characters. -- if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') { -- if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) { -- fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n", -- a_char, name); -- } -- } else { -- // skip check if unknown alph -- if (alph != NULL && !alph_is_known(alph, a_char)) { -- fprintf(stderr, "Warning: Converting illegal character %c to %c ", -- a_char, alph_wildcard(alph)); -- fprintf(stderr, "in sequence %s.\n", name); -- a_char = alph_wildcard(alph); -- } -- raw_sequence[offset] = (char) a_char; -- ++offset; -- } -- } -- -- raw_sequence[offset] = '\0'; -- free_data_block(seq_block); -- return(return_value); --} -- --/**************************************************************************** - * Read one sequence from a file in Fasta format. - * - * Return: Was a sequence successfully read? -@@ -320,44 +266,6 @@ - } - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T *sequence --) { -- -- assert(sequence != NULL); -- assert(get_seq_length(sequence) <= max_size); -- -- // Get the raw sequence buffer from the SEQ_T -- char *raw_sequence = get_raw_sequence(sequence); -- if (raw_sequence == NULL) { -- // Allocate space for raw sequence if not done yet. -- raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -- raw_sequence[0] = 0; -- } -- -- // Read a block of sequence charaters into the -- // raw sequence buffer for the SEQ_T. -- char *name = get_seq_name(sequence); -- BOOLEAN_T is_complete = read_raw_sequence_from_reader( -- fasta_reader, -- name, -- NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable! -- buffer_offset, -- max_size, -- raw_sequence -- ); -- set_raw_sequence(raw_sequence, is_complete, sequence); -- --} -- --/**************************************************************************** - * Read all the sequences from a FASTA file at once. - Multiple files can be appended by calling this more than once. - ****************************************************************************/ ---- a/src/fasta-io.h -+++ b/src/fasta-io.h -@@ -43,19 +43,6 @@ - ); - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T* sequence --); -- -- --/**************************************************************************** - * Read all the sequences from a file in Fasta format. - ****************************************************************************/ - void read_many_fastas ---- a/src/init.c -+++ b/src/init.c -@@ -767,10 +767,16 @@ - if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins - plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB); - } else { -- fprintf(stderr, "The prior library must be specified for DNA or custom " -- "alphabets when specifiying a prior type of 'dmix', 'mega' " -- "or 'megap'."); -- exit(1); -+ fprintf( -+ stderr, -+ "WARNING: When using DNA or a custom alphabet, " -+ "and specifiying a prior type of\n" -+ "'dmix', 'mega' or 'megap', a prior library must be provided.\n" -+ "No prior library was provided, so a simple Dirichlet prior will be used.\n" -+ ); -+ prior = "dirichlet"; -+ ptype = Dirichlet; -+ if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet - } - } - } ---- a/src/seq-reader-from-fasta.c -+++ b/src/seq-reader-from-fasta.c -@@ -639,11 +639,140 @@ - return fasta_reader->current_position; - } - -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+) { -+ -+ -+ assert(sequence != NULL); -+ assert(offset < max_size); -+ -+ // Get the raw sequence buffer from the SEQ_T -+ char *raw_sequence = get_raw_sequence(sequence); -+ if (raw_sequence == NULL) { -+ // Allocate space for raw sequence if not done yet. -+ raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -+ raw_sequence[0] = 0; -+ } -+ -+ // Read a block of sequence charaters into the -+ // raw sequence buffer for the SEQ_T, starting at offset. -+ BOOLEAN_T is_complete = read_raw_sequence_from_reader( -+ fasta_reader, -+ max_size - offset, -+ raw_sequence + offset -+ ); -+ set_raw_sequence(raw_sequence, is_complete, sequence); -+} -+ -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence buffer. -+) { -+ -+ SEQ_READER_FROM_FASTA_T *fasta_reader -+ = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader); -+ -+ // Read sequence into temp. buffer from the sequence file. -+ char buffer[max_chars]; -+ long start_file_pos = ftell(fasta_reader->fasta_file); -+ size_t seq_index = 0; -+ size_t total_read = 0; -+ while (seq_index < max_chars) { -+ -+ size_t num_char_read = fread( -+ buffer, -+ sizeof(char), -+ max_chars - seq_index, -+ fasta_reader->fasta_file -+ ); -+ fasta_reader->current_position += num_char_read; -+ total_read += num_char_read; -+ -+ if (feof(fasta_reader->fasta_file)) { -+ fasta_reader->at_end_of_file = TRUE; -+ } -+ else if (num_char_read < (max_chars - seq_index)) { -+ die( -+ "Error while reading sequence from file:%s.\nError message: %s\n", -+ fasta_reader->filename, -+ strerror(ferror(fasta_reader->fasta_file)) -+ ); -+ } -+ -+ size_t i; -+ for(i = 0; i < num_char_read; ++i) { -+ char c = buffer[i]; -+ assert(c != 0); -+ if (isspace(c)) { -+ // Skip over white space -+ fasta_reader->at_start_of_line = (c == '\n'); -+ } -+ else if (c == '>' && fasta_reader->at_start_of_line == TRUE) { -+ // We found the start of a new sequence while trying -+ // to fill the buffer. Leave the buffer incomplete. -+ // and wind back the file -+ fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET); -+ fasta_reader->current_position = start_file_pos + i - 1; -+ fasta_reader->at_end_of_seq = TRUE; -+ fasta_reader->at_start_of_line = FALSE; -+ fasta_reader->at_end_of_file = FALSE; -+ break; -+ } -+ else { -+ fasta_reader->at_start_of_line = FALSE; -+ // Check that character is legal in alphabet. -+ // If not, replace with wild card character. -+ if (alph_is_known(fasta_reader->alphabet, c)) { -+ raw_sequence[seq_index] = c; -+ } -+ else { -+ raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet); -+ fprintf( -+ stderr, -+ "Warning: %c is not a valid character in %s alphabet.\n" -+ " Converting %c to %c.\n", -+ c, -+ alph_name(fasta_reader->alphabet), -+ c, -+ raw_sequence[i] -+ ); -+ } -+ ++seq_index; -+ } -+ } -+ if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) { -+ break; -+ } -+ } -+ -+ raw_sequence[seq_index] = '\0'; -+ return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file); -+} -+ - /****************************************************************************** -- * Fills in the next data block for the sequence. -- * During the first call for the sequence it fills in the full data block. -- * On successive calls, shifts the sequence in the block down one position -- * and reads one more character. -+ * Populates the data block for the with the next block of sequence. -+ * -+ * During the first call for the sequence it fills in a buffer from a file, -+ * The sequence pointer in the data block is set to point at the start of the buffer. -+ * On successive calls, the sequence pointer in the block is shifted down one position -+ * in the buffer. When the end of the buffer is reached, it is filled again from the file. - * - * Returns TRUE if it was able to completely fill the block, FALSE if - * the next sequence or EOF was reached before the block was filled. ---- a/src/seq-reader-from-fasta.h -+++ b/src/seq-reader-from-fasta.h -@@ -37,5 +37,30 @@ - int * end_ptr // end position of sequence (chr:\d+-(\d+)) - ); - -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence. -+); -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+); -+ -+ - size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader); - #endif diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch deleted file mode 100644 index 498d1df7b664..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -15,6 +15,21 @@ - -

    MEME Suite Release Notes

    -
    -+ MEME version 4.11.2 patch 2 -- October 24, 2016 -+
      -+
    • -+ Bug fixes -+
        -+
      • -+ Fixed bug in handling of RNA-like custom alphabets. -+
        • -+
      • -+ Fixed bug in MAST -comp option. -+
        • -+
      -+
    -+
    - MEME version 4.11.2 patch 1 -- June 16, 2016 -
      -
    • ---- a/src/alph-in.c -+++ b/src/alph-in.c -@@ -1044,7 +1044,7 @@ - lookup[0] = sym->complement; - comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup); - } -- if (comp1 != comp2) { -+ if (comp1 && (comp1 != comp2)) { - add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, - "not like %s alphabet as %c complement rules are incorrect", - ext_name, req_syms[i])); ---- a/src/mast-util.c -+++ b/src/mast-util.c -@@ -740,14 +740,14 @@ - - // create the frequency array - alph = xlate ? xlate_dest_alph(xlate) : alph; -- freq = allocate_array(alph_size_core(alph)); -+ freq = allocate_array(alph_size_full(alph)); - init_array(0, freq); - - // count the number of letters of each type - if (xlate) { - for (n=0; sequence[n]; n++) { - i = xlate_index(xlate, false, sequence+n); -- if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq); -+ if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq); - } - } else { - for (n=0; sequence[n]; n++) { diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild deleted file mode 100644 index 0f7d25b43368..000000000000 --- a/sci-biology/meme/meme-4.11.2_p2.ebuild +++ /dev/null @@ -1,109 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools perl-functions python-single-r1 versionator - -MY_PV=$(get_version_component_range 1-3) -MY_P=${PN}_${MY_PV} - -DESCRIPTION="The MEME/MAST system - Motif discovery and search" -HOMEPAGE="http://meme-suite.org/tools/meme" -SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz" - -LICENSE="meme" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples mpi" - -RDEPEND=" - ${PYTHON_DEPS} - app-shells/tcsh - dev-libs/libxml2:2 - dev-libs/libxslt - sys-libs/zlib - app-text/ghostscript-gpl - media-gfx/imagemagick - dev-lang/perl:= - dev-perl/HTML-Parser - dev-perl/HTML-Template - dev-perl/Log-Log4perl - dev-perl/Math-CDF - dev-perl/XML-Compile-SOAP - dev-perl/XML-Compile-WSDL11 - dev-perl/XML-Parser - dev-perl/XML-Simple - virtual/perl-Data-Dumper - virtual/perl-Exporter - virtual/perl-File-Path - virtual/perl-File-Spec - virtual/perl-File-Temp - virtual/perl-Getopt-Long - virtual/perl-Scalar-List-Utils - virtual/perl-Time-HiRes - mpi? ( virtual/mpi )" -DEPEND="${RDEPEND}" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -S="${WORKDIR}/${MY_P}" -PATCHES=( - "${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch - "${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch - "${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch -) - -pkg_setup() { - python-single-r1_pkg_setup - perl_set_version -} - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - --sysconfdir="${EPREFIX}"/etc/${PN} \ - --with-logs="${EPREFIX}"/var/log/${PN} \ - --with-perl=perl \ - --with-convert=convert \ - --with-gs=gs \ - --disable-build-libxml2 \ - --disable-build-libxslt \ - $(use_enable debug) \ - $(use_enable doc) \ - $(use_enable examples) \ - $(use_enable !mpi serial) \ - --with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \ - PYTHON="${EPYTHON}" - - # delete bundled libs, just to be sure. These need - # to be removed after econf, else AC_OUTPUT will fail - rm -r src/{libxml2,lib{,e}xslt} || die -} - -src_test() { - # bug #297070 - emake -j1 test -} - -src_install() { - default - docompress -x /usr/share/doc/${PF}/examples - - # prefix all binaries with 'meme-', in order - # to prevent collisions, bug 455010 - cd "${ED%/}"/usr/bin/ || die - local i - for i in *; do - if [[ $i != meme-* ]]; then - mv {,meme-}"${i}" || die - fi - done - - keepdir /var/log/meme -} diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/meme/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest index 9e311756e1fc..d4178fd5bb6a 100644 --- a/sci-biology/muscle/Manifest +++ b/sci-biology/muscle/Manifest @@ -1,4 +1,4 @@ -AUX 3.8.31-make.patch 989 BLAKE2B 1cbbee37b5c88a34705fd2adb78d4c5c1533a18f1896f3e4d909e17d15dbf5ccd5308137dd3a94f17ede40b637c9309e0694353e8f8e6c6c55cc966ebd4b52ef SHA512 e528b032d4e60d2ca22de1129da56125b8915ed288ee25965b2bc5b1d6118d1d589fa632dac9829011a405c3189b8b6b6c056eedde9dd30a9b6a6f572a5e2d2c +AUX 3.8.31-make.patch 922 BLAKE2B 57f112a4538b1b0a791f9e151e0e27ba8c6af2beefb6ce95f064edd183315e17a09d92a9cd0a368907e2b4a1571463669e5ef83e96758603fa4807780ea98bc0 SHA512 c948991ab4f7b7d6e05ab63df00ea6ac576587e63f808c377cc86f4e3863c7cee207569d7f0a8572a8fcf81f2e23d9dd6b1270447a0028910301d74554ab1fac DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B 79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce -EBUILD muscle-3.8.31.ebuild 602 BLAKE2B fb70469bb54d0002cc73e364334355ffc3888248cf51ee59ec466cff5145380de0285601cdb20a91af068368fb2c3414d91bcb82a93dee9fb84d5b3bb6f565f1 SHA512 4167a3402188bc2b17baa5419fae65e1a10c5884d8419de929434e3d44d985889a5131d34dae3854bc58e25450ccbc055d38839255a8153eb2e4d19ae3b84253 +EBUILD muscle-3.8.31.ebuild 580 BLAKE2B d9ccdea4e8e87b89c107d019c7b1ac87ecadf16a92c093e488e7121f6438de4cf003ffe0114402b3b7c90b08e484216908bb01e950f49f014ac748af259dcf58 SHA512 2295bd95b0388e43d2209d37bc48f69a3937bb1a568003f00a66709bea980bc5598f632bf301852149bba24d1d782e86ffca5cc066367f0a3791cd51a6aef3e5 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch index 7c0e7308df54..fa3f5c3a014b 100644 --- a/sci-biology/muscle/files/3.8.31-make.patch +++ b/sci-biology/muscle/files/3.8.31-make.patch @@ -1,7 +1,5 @@ -diff --git a/src/mk b/src/mk -index 475d25a..d4b7e83 100755 ---- a/src/mk -+++ b/src/mk +--- a/mk ++++ b/mk @@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt for CPPName in $CPPNames diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild index 1e62a9d28eee..72c9a2c7e178 100644 --- a/sci-biology/muscle/muscle-3.8.31.ebuild +++ b/sci-biology/muscle/muscle-3.8.31.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_P="${PN}${PV}_src" @@ -14,19 +14,18 @@ SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 ppc x86" -IUSE="" RDEPEND="!sci-libs/libmuscle" -DEPEND="" S="${WORKDIR}"/${PN}${PV}/src -src_prepare() { - epatch "${FILESDIR}"/${PV}-make.patch +PATCHES=( "${FILESDIR}"/${PV}-make.patch ) + +src_configure() { tc-export CXX } src_install() { - dobin "${PN}" + dobin muscle dodoc *.txt } diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest index d20aa9ef0fb6..53dda9d90de9 100644 --- a/sci-biology/newick-utils/Manifest +++ b/sci-biology/newick-utils/Manifest @@ -1,3 +1,5 @@ +AUX newick-utils-1.6-deduplicate-libnw.patch 5843 BLAKE2B ce36e9b1160ccd2d41a29c28626086fc713d1bd24ce5d93b9def21780bac7275bcde87e3c39a51cfb8bc5db6f99094ab9412b25fcedbab6bac7ab14720c89eac SHA512 e189a53f97fc2a31305c1d8c52d088fe0a80031d3328fafbebdc8371d6ff030b1aa71ae008981c591519888457c345281986d0130653b60e492a19d063a957ba +AUX newick-utils-1.6-fno-common.patch 1359 BLAKE2B ccc59ad91d69ac2268d26e6704eeafc15c65e883bf8292ddfa6f1f5e75ef368238cbb38dea7f18fdafbb390d4e916fae1184ff89d8746ae98dfd5d759be69154 SHA512 9f6e53485e5d6872393bbf6404a112a105cde6d2e8993bb0c28b73be0458ce64a438eb574b451eefad28076a63ef82b0d204e3e78e301543d320f0e7b34b7799 DIST newick-utils-1.6.tar.gz 7518535 BLAKE2B 6b5456be6fec4311e40b19972736194a3f2eb51e8efc4a97cdcf027838459a8f22f41d10e49e7ac3e6461aa290aeed1813baeffcb5706749ebf1bf4333e28047 SHA512 1e327f9a32b5b0df097bcb63f933f9073a85f0499a2a48be122f4affca52ae1541e1a6e0cca7420447aa8fe8d10d6e76e8d89933b2f84e023d6c87b50808d96c -EBUILD newick-utils-1.6.ebuild 399 BLAKE2B d7e3abeeb7c9abd0677733ec78edfbca2d036766a733d7fb5c89bc12280f0a48c24a841e09b31185c100f750c36a55252f51c287287de5baa3b01a1cc14a54fa SHA512 f359ffd190bf1631108c84ea5230e629b7aa3aa8426d9f3e49b5df4c7d22a75e29bb74215144ab7dfa506dbbec704164c80c58b57c87305314e320c62d764c8d -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 +EBUILD newick-utils-1.6-r1.ebuild 733 BLAKE2B 60cf97660294c13efba331d06d299ed21761446981e62832bf5d9fdb713196fa10f2713f0cd33e89c1dd31e5829decca3ce919806fbf92a5652e30cee4e10c6f SHA512 b6f9daeecf7035a145e53feeb9b70676154412dea04861f1093862fb0f943a2d3f26cb791506918f1f12596abe31680ce0a13081e88494270d295d5d5d70cf74 +MISC metadata.xml 355 BLAKE2B cabdb6f1dd0f44f079f81789daa15b311048672fc5b4a3e50f408a4f0a22abc30f9d20c24c34d8fdf5308ff6c18942438eca19b78540828999b506ac9f710430 SHA512 a9f72bde780552c341f039ac78d91c4958148b135a7944c232e5755edb54c064e8bb5107f54e39be798bedf0601ffaa60a0ff137709bc6b5c3a2fb65e4fe49bc diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch new file mode 100644 index 000000000000..ca997830aced --- /dev/null +++ b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch @@ -0,0 +1,153 @@ +Don't rebuild all of libnw.la pointlessly + +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -8,6 +8,8 @@ + showsrc: + @echo $(srcdir) + ++LDADD = $(top_builddir)/src/libnw.la ++ + TESTS = test_newick_scanner test_newick_parser test_rnode test_list \ + test_link test_masprintf test_svg_graph_radial \ + test_canvas test_concat test_hash test_lca test_enode \ +@@ -37,100 +39,57 @@ + + SRC = $(top_builddir)/src + +-test_newick_scanner_SOURCES = test_newick_scanner.c $(SRC)/newick_scanner.c \ +- $(SRC)/newick_parser.c $(SRC)/rnode.c $(SRC)/rnode_iterator.c \ +- $(SRC)/list.c $(SRC)/hash.c $(SRC)/masprintf.c $(SRC)/link.c +- +-test_newick_parser_SOURCES = test_newick_parser.c $(SRC)/parser.c \ +- $(SRC)/newick_scanner.c $(SRC)/newick_parser.c $(SRC)/list.c \ +- $(SRC)/rnode.c $(SRC)/link.c $(SRC)/hash.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c $(SRC)/to_newick.c $(SRC)/concat.c +- +-test_rnode_SOURCES = test_rnode.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \ +- tree_stubs.c $(SRC)/nodemap.c $(SRC)/link.c +- +-test_list_SOURCES = test_list.c $(SRC)/list.c +- +-test_link_SOURCES = test_link.c $(SRC)/link.c $(SRC)/nodemap.c \ +- $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/rnode.c \ +- $(SRC)/concat.c $(SRC)/hash.c tree_stubs.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c ++test_newick_scanner_SOURCES = test_newick_scanner.c ++ ++test_newick_parser_SOURCES = test_newick_parser.c ++ ++test_rnode_SOURCES = test_rnode.c tree_stubs.c ++ ++test_list_SOURCES = test_list.c ++ ++test_link_SOURCES = test_link.c tree_stubs.c + + test_canvas_SOURCES = test_canvas.c $(SRC)/canvas.c + +-test_concat_SOURCES = test_concat.c $(SRC)/concat.c ++test_concat_SOURCES = test_concat.c ++ ++test_hash_SOURCES = test_hash.c ++ ++test_lca_SOURCES = test_lca.c tree_stubs.c ++ ++test_nodemap_SOURCES = test_nodemap.c tree_stubs.c + +-test_hash_SOURCES = test_hash.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c ++test_to_newick_SOURCES = test_to_newick.c tree_stubs.c + +-test_lca_SOURCES = test_lca.c $(SRC)/lca.c $(SRC)/list.c $(SRC)/nodemap.c \ +- $(SRC)/link.c $(SRC)/rnode.c $(SRC)/hash.c \ +- $(SRC)/rnode_iterator.c tree_stubs.c $(SRC)/masprintf.c \ +- $(SRC)/error.c +- +-test_nodemap_SOURCES = test_nodemap.c $(SRC)/nodemap.c \ +- $(SRC)/rnode.c $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c tree_stubs.c +- +-test_to_newick_SOURCES = test_to_newick.c $(SRC)/to_newick.c \ +- $(SRC)/rnode.c $(SRC)/link.c $(SRC)/concat.c \ +- $(SRC)/list.c $(SRC)/rnode_iterator.c $(SRC)/hash.c \ +- $(SRC)/masprintf.c $(SRC)/parser.c $(SRC)/newick_scanner.c \ +- $(SRC)/newick_parser.c tree_stubs.c +- +-test_tree_SOURCES = test_tree.c $(SRC)/tree.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/to_newick.c $(SRC)/nodemap.c $(SRC)/link.c $(SRC)/concat.c \ +- $(SRC)/hash.c tree_stubs.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c +- +-test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c \ +- $(SRC)/hash.c $(SRC)/rnode.c $(SRC)/list.c $(SRC)/link.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c +- +-test_enode_SOURCES = test_enode.c $(SRC)/enode.c $(SRC)/rnode.c \ +- $(SRC)/link.c $(SRC)/list.c $(SRC)/rnode_iterator.c \ +- $(SRC)/hash.c $(SRC)/masprintf.c +- +-test_rnode_iterator_SOURCES = test_rnode_iterator.c $(SRC)/rnode_iterator.c \ +- $(SRC)/list.c $(SRC)/link.c $(SRC)/rnode.c $(SRC)/to_newick.c \ +- $(SRC)/hash.c $(SRC)/nodemap.c tree_stubs.c $(SRC)/masprintf.c \ +- $(SRC)/parser.c $(SRC)/newick_scanner.c $(SRC)/newick_parser.c \ +- $(SRC)/concat.c ++test_tree_SOURCES = test_tree.c tree_stubs.c ++ ++test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c ++ ++test_enode_SOURCES = test_enode.c $(SRC)/enode.c ++ ++test_rnode_iterator_SOURCES = test_rnode_iterator.c tree_stubs.c + + test_readline_SOURCES = test_readline.c $(SRC)/readline.c + +-test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c \ +- $(SRC)/rnode.c $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/link.c \ +- $(SRC)/concat.c $(SRC)/rnode_iterator.c \ +- $(SRC)/hash.c $(SRC)/masprintf.c +- +-test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c \ +- $(SRC)/masprintf.c +- +-test_masprintf_SOURCES = test_masprintf.c $(SRC)/masprintf.c +- +-test_error_SOURCES = test_error.c $(SRC)/error.c +- +-test_order_tree_SOURCES = test_order_tree.c $(SRC)/order_tree.c tree_stubs.c \ +- $(SRC)/link.c $(SRC)/to_newick.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/masprintf.c $(SRC)/concat.c $(SRC)/hash.c $(SRC)/nodemap.c \ +- $(SRC)/rnode_iterator.c +- +-test_graph_common_SOURCES = test_graph_common.c $(SRC)/graph_common.c \ +- tree_stubs.c $(SRC)/link.c $(SRC)/list.c $(SRC)/tree.c \ +- $(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \ +- $(SRC)/rnode.c $(SRC)/nodemap.c ++test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c ++ ++test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c ++ ++test_masprintf_SOURCES = test_masprintf.c ++ ++test_error_SOURCES = test_error.c ++ ++test_order_tree_SOURCES = test_order_tree.c tree_stubs.c $(SRC)/order_tree.c ++ ++test_graph_common_SOURCES = test_graph_common.c tree_stubs.c $(SRC)/graph_common.c + + test_svg_graph_radial_SOURCES = test_svg_graph_radial.c \ +- $(SRC)/svg_graph_radial.c $(SRC)/tree.c $(SRC)/svg_graph.c \ +- $(SRC)/rnode.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c \ +- $(SRC)/rnode_iterator.c $(SRC)/svg_graph_ortho.c $(SRC)/error.c \ ++ $(SRC)/svg_graph_radial.c $(SRC)/svg_graph.c \ ++ $(SRC)/svg_graph_ortho.c \ + $(SRC)/readline.c $(SRC)/xml_utils.c $(SRC)/graph_common.c \ +- $(SRC)/node_pos_alloc.c $(SRC)/nodemap.c $(SRC)/lca.c $(SRC)/link.c ++ $(SRC)/node_pos_alloc.c + +-test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c $(SRC)/rnode.c \ +- $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c $(SRC)/nodemap.c ++test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c + + clean-local: + $(RM) *.out diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch new file mode 100644 index 000000000000..15847a52c480 --- /dev/null +++ b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch @@ -0,0 +1,41 @@ +--- a/src/address_parser.c ++++ b/src/address_parser.c +@@ -83,6 +83,8 @@ + #include "enode.h" + #include "address_parser_status.h" + ++enum address_parser_status_type address_parser_status; ++ + extern int adslex (void); + + /* The root of the expression (when represented as a parse tree) */ +--- a/src/address_parser_status.h ++++ b/src/address_parser_status.h +@@ -13,4 +13,4 @@ + * returns either \c NULL or the top-level enode of the address, so we need to + * use an extern variable to convey its status. */ + +-enum address_parser_status_type address_parser_status; ++extern enum address_parser_status_type address_parser_status; +--- a/tests/test_newick_parser.c ++++ b/tests/test_newick_parser.c +@@ -11,7 +11,7 @@ + int nwslex (void); + struct rnode *root; + struct llist *nodes_in_order; +-enum parser_status_type newick_parser_status; ++extern enum parser_status_type newick_parser_status; + void newick_scanner_set_string_input(char *); + + /* NOTE: we can use to_newick() to check the parser's output because this +--- a/tests/test_newick_scanner.c ++++ b/tests/test_newick_scanner.c +@@ -20,7 +20,7 @@ + int nwslex (void); + struct rnode *root; + struct llist *nodes_in_order; +-enum parser_status_type newick_parser_status; ++extern enum parser_status_type newick_parser_status; + void newick_scanner_set_string_input(char *); + void newick_scanner_set_file_input(FILE *); + diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml index 959160fe46b1..d9bc91509874 100644 --- a/sci-biology/newick-utils/metadata.xml +++ b/sci-biology/newick-utils/metadata.xml @@ -1,8 +1,11 @@ - - sci-biology@gentoo.org - Gentoo Biology Project - + + sci-biology@gentoo.org + Gentoo Biology Project + + + Uses dev-libs/libxml2 to handle ornaments + diff --git a/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild new file mode 100644 index 000000000000..3dcb438832a2 --- /dev/null +++ b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit autotools + +DESCRIPTION="Tools for processing phylogenetic trees" +HOMEPAGE="http://cegg.unige.ch/newick_utils" +SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="xml" + +DEPEND=" + xml? ( dev-libs/libxml2 )" +RDEPEND=" + ${DEPEND} + !dev-games/libnw" + +PATCHES=( + "${FILESDIR}"/${P}-deduplicate-libnw.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --disable-static \ + --without-guile \ + --without-lua \ + $(use_with xml libxml) +} + +src_install() { + default + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-biology/newick-utils/newick-utils-1.6.ebuild b/sci-biology/newick-utils/newick-utils-1.6.ebuild deleted file mode 100644 index 845bc0116205..000000000000 --- a/sci-biology/newick-utils/newick-utils-1.6.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="Tools for processing phylogenetic trees" -HOMEPAGE="http://cegg.unige.ch/newick_utils" -SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="!dev-games/libnw" - -src_test() { - emake -C tests check-TESTS -} diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest index 02b763e3dba9..e0f9ddd35a94 100644 --- a/sci-biology/paml/Manifest +++ b/sci-biology/paml/Manifest @@ -1,3 +1,5 @@ -DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a -EBUILD paml-4.4c-r1.ebuild 983 BLAKE2B 4c4da7c1bdfdb0f479b65b27c39463d3797384e69e11929e446e867a741a8d49102842aad00a3187abd119885fa23879f4c13128577d64de23b6011455271352 SHA512 a7d590056e148c08607c6c15e872f6fc4ea87166336f19eeef497efb4852481b782b83f8e40b6f50005dffaa45b1fb6d028cd101fd54efa643e3678e60836b04 +AUX paml-4.9j-fno-common.patch 521 BLAKE2B 93dda51495e65cde9b3e92379e43756c5efe77953b114ceb88c8dc9ae6453d5b2742e250cf9a2d6feec3e86ff430417a4ecd8fd06b199a899b14d0aeac5199e2 SHA512 c24431264c7a69077f9ea9f511e93d45ac8adc4a5cc41446ca96de4e270b918543fb1a424b9119bc1723b2a9574434321a55a5af88712e0f3d51ef5c964575fb +AUX paml-4.9j-makefile.patch 1540 BLAKE2B 9ffa0f8fab089d26e325688596975944a10e9e62ba1554b532b3f31c7f508b5b1001f5481ad9b8ae7fa97ffd8bcdffda3c285935c8efa3442175f4686e0a44ad SHA512 51b05e865ff68d58cf0f8cc2bc23e8e90e5d12ac8daceb96ac9cc64fdf75c704b5b16b6b8248a0e3cd03c1b18e5bbb61727c281ad46b4988a197f695b464c80d +DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758 +EBUILD paml-4.9j.ebuild 843 BLAKE2B 8f92ab034a78571de1bccecc21d04fc9eef7414d98c5a3f4a6d4a96f59ddcd32e0c0c1c82928ed3949f7c64a493fbf5c3962016425ab8bcef6b3718cf50e49ba SHA512 74100d6e6a0913c0c1a56039468b5a78c86fc13fab054a0dc6fe307ba975f84865c999f5472c1e18a5bf28c7f0fe37359f3c557965b251968eba692bec49e607 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch new file mode 100644 index 000000000000..66eeb8a56b86 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-fno-common.patch @@ -0,0 +1,14 @@ +--- a/src/paml.h ++++ b/src/paml.h +@@ -372,9 +372,9 @@ + void printSptree(void); + + +-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; ++typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; + +-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; ++typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; + + + /* use mean (0; default) for discrete gamma instead of median (1) */ diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch new file mode 100644 index 000000000000..611b80444c89 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-makefile.patch @@ -0,0 +1,42 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,27 +1,18 @@ +-PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2 +-CC = cc # cc, gcc, cl ++PRGS = baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2 + +-CFLAGS = -O3 ++CFLAGS += -Wno-unused-result + #CFLAGS = -fast + +-LIBS = -lm # -lM ++LDLIBS = -lm + + all : $(PRGS) + +-baseml : baseml.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS) +-basemlg : basemlg.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS) +-codeml : codeml.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS) +-evolver : evolver.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS) +-pamp : pamp.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS) +-mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS) +- $(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS) +-yn00: yn00.c tools.c paml.h +- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS) +-chi2 : chi2.c +- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS) ++baseml: tools.o paml.h ++basemlg: tools.o paml.h ++codeml: tools.o paml.h ++evolver: tools.o paml.h ++pamp: tools.o paml.h ++mcmctree: tools.o paml.h ++infinitesites: tools.o paml.h ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS) ++yn00: tools.o paml.h diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild deleted file mode 100644 index 27fe5ed4c769..000000000000 --- a/sci-biology/paml/paml-4.4c-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs versionator - -MY_P=$(version_format_string '${PN}$1$2') - -DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" -HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" -SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz" - -LICENSE="free-noncomm" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S=${WORKDIR}/${MY_P} - -src_prepare() { - # Notice send by mail to prof. Ziheng Yang - sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608 -} - -src_compile() { - emake -C src \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dodoc README.txt doc/* - - insinto /usr/share/${PN}/control - doins *.ctl - - insinto /usr/share/${PN}/dat - doins stewart* *.dat dat/* - - insinto /usr/share/${PN} - doins -r examples/ - - cd src || die - dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 -} diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild new file mode 100644 index 000000000000..e8a5d07ee40c --- /dev/null +++ b/sci-biology/paml/paml-4.9j.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${P/-/}" +PATCHES=( + "${FILESDIR}"/${PN}-4.9j-makefile.patch + "${FILESDIR}"/${PN}-4.9j-fno-common.patch +) + +src_configure() { + tc-export CC +} + +src_compile() { + emake -C src +} + +src_install() { + dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2} + + dodoc -r README.txt doc/. + + insinto /usr/share/${PN}/control + doins *.ctl + + insinto /usr/share/${PN}/dat + doins -r stewart* *.dat dat/. + + insinto /usr/share/${PN} + doins -r examples +} diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest index 4a74a1a8a1f8..c88142631f51 100644 --- a/sci-biology/phylip/Manifest +++ b/sci-biology/phylip/Manifest @@ -1,7 +1,6 @@ AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed4784494a6a4c9bb12a451223c0ff81ae3ba80da81f4d8d3a00a21cad557f575a81325a180a819c0e SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a -DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d -DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be -EBUILD phylip-3.69-r1.ebuild 1146 BLAKE2B 690bd802cb7ed4dce34de3c272357df93c528881efe5b40c8b4e3f6c281791eb6809559a5f1680da55d5c9466cac666d290722a513eb3364245bf5f6bcd9204e SHA512 7e7eada3c9c1b6ae479360749d40943ec977505986871ffe8f5972604e2834aaddfd015f49b9e60f3f3292f8e98f410fdeecd240f34a47b86046972f067111c5 -EBUILD phylip-3.696-r1.ebuild 1130 BLAKE2B 94c4b4213d24b46fe60f3d180a1d8a742f9c173f5482e18e1521b0f3e61ac2738038c5a558fdbdeaece2f9887e08796d6981bc3ff54bec2e60dfb0ebffa7d156 SHA512 02e33c7a34910a006fb0e63d9cac40b9e71446b5b64185b968d46fdcb78217c4f2bdfe02b96ae2eefe10839e892c2c533581e9d149cfc63f1d64b2b87b1416a9 -EBUILD phylip-3.696-r2.ebuild 1204 BLAKE2B d6fcbe08f0528d657bc30da9c61c67571ee403c7f15caec8a86d2ed9a75958e471f8b2582d39c86f1ddb675636bf9d211665d398593651c968b9d87b9fac4a2a SHA512 2827584e9293a5bc95087c0d3f19b4d0ac1a7ecac6b5b81738abb16ee007d65ab91e14baf0885578afc4c369841456583d88ee51bf0738b3d04d4924eb086e5c +AUX phylip-3.698-fno-common.patch 1934 BLAKE2B 613149dd930aa3efc921d5844e97c76475bffaedfe701d46ae980a4fabd0896d6d81fde4722599217508689d41ec70e110cbf0638abad13b2c0dbbf1c6c2f159 SHA512 4e89f330338da601ac7311995a341cab235288d82b9a63ba632b830eb99052191a920f51f43236c1a71f07ce3e427dd58ff5bc0004d1ed4ebbea8bf223390aa1 +AUX phylip-3.698-makefile.patch 9481 BLAKE2B fc8b863c05953333588f174251e40a86138a5cf2b08206861bef594ebea1d7d63b53895517bb6916e1c06c700b379cd93e76a673af4ec225502ac886dbe702d5 SHA512 6713644543f676dd6b21408675ac65c38f6a2fed4bd04619c19de881e5269e4c0bb89e440cf59dd0f1f13ad72cbbf420baccdaeb6a0c7a2a807895f87376d76f +DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d +EBUILD phylip-3.698.ebuild 1193 BLAKE2B c196d7cdfe79a17691c2fe5567a30c0b937015ef3f8f1ce11a317dd1c86913487e6ac9a80f6ec21b80be804e7fcc1193522d3c4879d32e7510e7a9b89f1ce3b3 SHA512 da567382dfd57d40fca30845346f6ae8a5ce1bf16475bb1bdd5a220eb47d629b9904d4e0e76797971fcb2cfa795cc69a1480292a262350eb891b407e44f00509 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch new file mode 100644 index 000000000000..986b1d9650ab --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch @@ -0,0 +1,70 @@ +--- a/src/draw.c ++++ b/src/draw.c +@@ -34,6 +34,11 @@ + + char fontname[LARGE_BUF_LENGTH]; + ++long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, ++ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor; ++ ++char afmfile[FNMLNGTH]; ++ + /* format of matrix: capheight, length[32],length[33],..length[256]*/ + + byte *full_pic ; +--- a/src/draw.h ++++ b/src/draw.h +@@ -52,10 +52,10 @@ + double intensity, x, y, z; + } vrmllighttype; + +-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, ++extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, + vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor; + +-char afmfile[FNMLNGTH]; ++extern char afmfile[FNMLNGTH]; + + double lengthtext(char *, long, char *, fonttype); + double heighttext(fonttype, char *); +--- a/src/drawtree.c ++++ b/src/drawtree.c +@@ -69,7 +69,7 @@ + uselengths, regular, rotate, empty, rescaled, + notfirst, improve, nbody, firstscreens, labelavoid; + boolean pictbold,pictitalic,pictshadow,pictoutline; +-boolean javarun; ++extern boolean javarun; + + striptype stripe; + plottertype plotter, oldplotter; +--- a/src/phylip.c ++++ b/src/phylip.c +@@ -34,6 +34,8 @@ + + #include "phylip.h" + ++boolean javarun; ++ + #ifdef WIN32 + #include + /* for console code (clear screen, text color settings) */ +--- a/src/phylip.h ++++ b/src/phylip.h +@@ -331,7 +331,7 @@ + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++extern boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -351,7 +351,6 @@ + extern long spp, words, bits; + extern boolean ibmpc, ansi, tranvsp; + extern naym *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch new file mode 100644 index 000000000000..f55ab98dd9cb --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch @@ -0,0 +1,266 @@ +--- a/src/Makefile.unx ++++ b/src/Makefile.unx +@@ -81,7 +81,6 @@ + #CC = cc + # + # To use GCC instead: +-CC = gcc + # + # ---------------------------------------------------------------------------- + # +@@ -91,7 +90,6 @@ + # + # + #A minimal one +-CFLAGS = + # + # A basic one for debugging + #CFLAGS = -g +@@ -220,7 +218,7 @@ + @echo "Done." + @echo "" + +-put: ++put: all + @echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)" + @mkdir -p $(EXEDIR) + @cp $(PROGS) $(EXEDIR) +@@ -270,195 +268,195 @@ + clique.o: clique.c disc.h phylip.h + + clique: clique.o disc.o phylip.o +- $(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique ++ $(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique + + cons.o: cons.c cons.h phylip.h + + consense.o: consense.c cons.h phylip.h + + consense: consense.o phylip.o cons.o +- $(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense ++ $(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense + + contml.o: contml.c cont.h phylip.h + + contml: contml.o cont.o phylip.o +- $(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml ++ $(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml + + contrast.o: contrast.c cont.h phylip.h + + contrast: contrast.o cont.o phylip.o +- $(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast ++ $(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast + + dnacomp.o: dnacomp.c seq.h phylip.h + + dnacomp: dnacomp.o seq.o phylip.o +- $(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp ++ $(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp + + dnadist.o: dnadist.c seq.h phylip.h + + dnadist: dnadist.o seq.o phylip.o +- $(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist ++ $(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist + + dnainvar.o: dnainvar.c seq.h phylip.h + + dnainvar: dnainvar.o seq.o phylip.o +- $(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar ++ $(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar + + dnaml.o: dnaml.c seq.h phylip.h + + dnaml: dnaml.o seq.o phylip.o +- $(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml ++ $(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml + + dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h + + dnamlk: dnamlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk ++ $(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk + + dnamove.o: dnamove.c seq.h moves.h phylip.h + + dnamove: dnamove.o seq.o moves.o phylip.o +- $(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove ++ $(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove + + dnapenny.o: dnapenny.c seq.h phylip.h + + dnapenny: dnapenny.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny ++ $(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny + + dnapars.o: dnapars.c seq.h phylip.h + + dnapars: dnapars.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars ++ $(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars + + dolmove.o: dolmove.c disc.h moves.h dollo.h phylip.h + + dolmove: dolmove.o disc.o moves.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove ++ $(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove + + dollop.o: dollop.c disc.h dollo.h phylip.h + + dollop: dollop.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop ++ $(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop + + dolpenny.o: dolpenny.c disc.h dollo.h phylip.h + + dolpenny: dolpenny.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny ++ $(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny + + draw.o: draw.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c + + draw2.o: draw2.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw2.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c + + drawgram.o: drawgram.c draw.h phylip.h +- $(CC) $(DFLAGS) -c drawgram.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c + + drawgram: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram ++ $(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram + + # needed by java +-libdrawgram.so: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawgram.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) + + drawtree.o: drawtree.c draw.h phylip.h +- $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c + + drawtree: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree ++ $(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree + + # needed by java +-libdrawtree.so: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawtree.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) + + factor.o: factor.c phylip.h + + factor: factor.o phylip.o +- $(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor ++ $(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor + + fitch.o: fitch.c dist.h phylip.h + + fitch: fitch.o dist.o phylip.o +- $(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch ++ $(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch + + gendist.o: gendist.c phylip.h + + gendist: gendist.o phylip.o +- $(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist ++ $(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist + + kitsch.o: kitsch.c dist.h phylip.h + + kitsch: kitsch.o dist.o phylip.o +- $(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch ++ $(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch + + mix.o: mix.c disc.h wagner.h phylip.h + + mix: mix.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix ++ $(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix + + move.o: move.c disc.h moves.h wagner.h phylip.h + + move: move.o disc.o moves.o wagner.o phylip.o +- $(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move ++ $(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move + + neighbor.o: neighbor.c dist.h phylip.h + + neighbor: neighbor.o dist.o phylip.o +- $(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor ++ $(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor + + pars.o: pars.c discrete.h phylip.h + + pars: pars.o discrete.o phylip.o +- $(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars ++ $(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars + + penny.o: penny.c disc.h wagner.h phylip.h + + penny: penny.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny ++ $(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny + + proml.o: proml.c seq.h phylip.h + + proml: proml.o seq.o phylip.o +- $(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml ++ $(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml + + promlk.o: promlk.c seq.h phylip.h mlclock.h printree.h + + promlk: promlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk ++ $(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk + + protdist.o: protdist.c seq.h phylip.h + + protdist: protdist.o seq.o phylip.o +- $(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist ++ $(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist + + protpars.o: protpars.c seq.h phylip.h + + protpars: protpars.o seq.o phylip.o +- $(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars ++ $(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars + + restdist.o: restdist.c seq.h phylip.h + + restdist: restdist.o seq.o phylip.o +- $(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist ++ $(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist + + restml.o: restml.c seq.h phylip.h + + restml: restml.o seq.o phylip.o +- $(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml ++ $(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml + + retree.o: retree.c moves.h phylip.h + + retree: retree.o moves.o phylip.o +- $(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree ++ $(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree + + seqboot.o: seqboot.c phylip.h + + seqboot: seqboot.o seq.o phylip.o +- $(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot ++ $(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot + + treedist.o: treedist.c cons.h phylip.h + + treedist: treedist.o phylip.o cons.o +- $(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist ++ $(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist + + + # ---------------------------------------------------------------------------- diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild deleted file mode 100644 index e54c75d9b356..000000000000 --- a/sci-biology/phylip/phylip-3.69-r1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="free-noncomm" -IUSE="" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND="x11-libs/libXaw" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - sed \ - -e "s/CFLAGS = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \ - -e "s/CC = cc/CC = $(tc-getCC)/" \ - -e "s/DC = cc/DC = $(tc-getCC)/" \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild deleted file mode 100644 index 85150acaf9cb..000000000000 --- a/sci-biology/phylip/phylip-3.696-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD-2" -IUSE="" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND="x11-libs/libXaw" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - mv Makefile.unx Makefile || die - sed \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 \ - CC="$(tc-getCC)" \ - DC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dolib.so exe/*so && rm exe/*so - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild deleted file mode 100644 index 66391e0e662d..000000000000 --- a/sci-biology/phylip/phylip-3.696-r2.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD-2" -IUSE="" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -# 'mix' tool collides with dev-lang/elixir, bug #537514 -RDEPEND="x11-libs/libXaw - !!dev-lang/elixir" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - mv Makefile.unx Makefile || die - sed \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 \ - CC="$(tc-getCC)" \ - DC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dolib.so exe/*so && rm exe/*so - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild new file mode 100644 index 000000000000..0a8ef8f815ec --- /dev/null +++ b/sci-biology/phylip/phylip-3.698.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +# 'mix' tool collides with dev-lang/elixir, bug #537514 +RDEPEND=" + x11-libs/libXaw + !dev-lang/elixir" +DEPEND="${RDEPEND} + x11-base/xorg-proto" +BDEPEND="app-arch/unzip" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_prepare() { + default + + mkdir fonts || die + # clear out old binaries + rm -r exe || die +} + +src_configure() { + tc-export CC + append-cflags -Wno-unused-result +} + +src_compile() { + emake -C src -f Makefile.unx all put +} + +src_install() { + mv exe/font* fonts || die "Font move failed" + mv exe/factor exe/factor-${PN} || die "Renaming factor failed" + + dolib.so exe/*so + rm exe/*so || die + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + docinto html + dodoc -r phylip.html doc + + insinto /usr/share/phylip + doins -r fonts +} diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest index 7085f0176e19..e4fd19dff774 100644 --- a/sci-biology/profphd/Manifest +++ b/sci-biology/profphd/Manifest @@ -1,6 +1,5 @@ AUX profphd-1.0.39-perl.patch 376 BLAKE2B 16911d2f6952f9740f3cd16121bf6dab5e5571ce1f7e5ac671dde719146e55f2735f2951629220fe56a93c1243e792ddd820978163023b44613d8d08d037cd6a SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e -DIST profphd-1.0.39.tar.xz 4406776 BLAKE2B 9ac4bccd1fedf04f9556ff6953452879fc8cf9deb92853214b2c8b5c0b1c4daf3e5e0044d10ded9540e9dd3f40a6fee3a25ae808fd1e94b90e0db23f3af7b6df SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b +AUX profphd-1.0.40-symlink.patch 793 BLAKE2B 98e5f001570522bb1643d3aad1f2497bd84035c932d19b1b9c90d2933b08eb7d2b6c1871b356205494494c8225fac3d6d697aaac6229885876c439679455f092 SHA512 7985c4743ade3b73a7fdd0c697c84c3b5fdcba3c33c66d1d6aab7d4493ca4d1197c4c438ef79f44667ed2c86e6ee9c789c36928430605aac6438d9e734e8c56a DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 -EBUILD profphd-1.0.39.ebuild 833 BLAKE2B c173db3f129f9aecf3c0d8da461ef24c07b8de59e1c7adae3e9c39f227951b889fbcb71b78deb6fe45a7850f41cfddf87004fad251fdbd0425b5a7d6f96d60e5 SHA512 a2e15d1bd08ffa70e966001cc1a9787e2ad4c736e4275dee7ea8695ff6b36869c6acc60b6ae3e1fc607f86adff8bd5ae518dac2004f6c3b9657c5a53a732a123 -EBUILD profphd-1.0.40.ebuild 841 BLAKE2B c9b34a5bd892bab4dcc868ea1c3a5404c99d6a10f82ac217ea315a2203d4f0a7c65372cf5714eb480003729931362afdeba13e21e80c4590e392cd14d0bffed4 SHA512 c08773dfc516365b2d75cd0f7869f8c1178a17921ebd65e5ea1b78c236449ea818ce3086e63fd43eeb0ed9b4919b48e7f9f9d1e5a148de5a8e63342bf45d2d9d +EBUILD profphd-1.0.40.ebuild 787 BLAKE2B 382eef046bb2eddcbd7e8dd8a798096f4719c4df589f8022c51cf07bc7e920c161b9c9dc8dde7ee92eca9d998cc98ddc3aecdcbaa3de533a42556ff2e382931d SHA512 c583b877a4c912e473231d74ec84bb25bcc9f6d90d466fce7b73b1701e205a2c2ab57039e12ad755b7f3a296e7d8b95f752bb308337d012084ec3ea3738a69d2 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch new file mode 100644 index 000000000000..7733d55af4a6 --- /dev/null +++ b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch @@ -0,0 +1,11 @@ +--- a/src/prof/Makefile ++++ b/src/prof/Makefile +@@ -40,7 +40,7 @@ + ./. $(DESTDIR)$(prefix)/share/profphd/prof/. + find $(DESTDIR)$(prefix)/share/profphd/prof/embl/phd.pl $(DESTDIR)$(prefix)/share/profphd/prof/scr/CONFprof.pl $(DESTDIR)$(prefix)/share/profphd/prof/prof $(DESTDIR)$(prefix)/share/profphd/prof/scr/lib/prof.pm \ + -type f -exec sed -i -e 's|__PREFIX__|$(prefix)|g;s|__VERSION__|$(VERSION)|;' {} \; +- rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/prof ++ rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/profphd + + install-neuralnet: + mkdir -p $(DESTDIR)$(prefix)/share/profphd/prof/embl/para && rsync -aC \ diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild deleted file mode 100644 index cacbc13cbdf2..000000000000 --- a/sci-biology/profphd/profphd-1.0.39.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Secondary structure and solvent accessibility predictor" -HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" -SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND="dev-lang/perl" -RDEPEND="${DEPEND} - dev-perl/librg-utils-perl - sci-libs/profnet - sci-libs/profphd-utils -" - -src_prepare() { - sed \ - -e '/ln -s/s:prof$:profphd:g' \ - -i src/prof/Makefile || die - epatch "${FILESDIR}"/${P}-perl.patch -} - -src_compile() { - emake prefix="${EPREFIX}/usr" -} - -src_install() { - emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install -} diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild index 8e24cebeb5f3..4f9a16a9fe9d 100644 --- a/sci-biology/profphd/profphd-1.0.40.ebuild +++ b/sci-biology/profphd/profphd-1.0.40.ebuild @@ -1,37 +1,33 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 - -inherit eutils +EAPI=7 DESCRIPTION="Secondary structure and solvent accessibility predictor" HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" -SLOT="0" LICENSE="GPL-2" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" DEPEND="dev-lang/perl" -RDEPEND="${DEPEND} +RDEPEND=" + ${DEPEND} dev-perl/librg-utils-perl sci-libs/profnet - sci-libs/profphd-utils -" + sci-libs/profphd-utils" -src_prepare() { - sed \ - -e '/ln -s/s:prof$:profphd:g' \ - -i src/prof/Makefile || die - epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch -} +PATCHES=( + "${FILESDIR}"/${PN}-1.0.39-perl.patch + "${FILESDIR}"/${PN}-1.0.40-symlink.patch +) src_compile() { - emake prefix="${EPREFIX}/usr" + emake prefix="${EPREFIX}"/usr } src_install() { - emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install + emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install + einstalldocs } diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest index 370ccb30d448..dd7a8e73e258 100644 --- a/sci-biology/seaview/Manifest +++ b/sci-biology/seaview/Manifest @@ -1,5 +1,5 @@ -DIST seaview_4.5.4.tar.gz 420608 BLAKE2B 14b044706440da88987cd6b546595497f2de61e8d03615bfce4634104914a56544a464b0abedc83e6c96329697dccb2087c2b1af5a1fdbf0d9bdc26418a49a75 SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301 +AUX seaview-4.6-Wreserved-user-defined-literal.patch 3271 BLAKE2B 695411acffed448ecc792753a9c8f969e4e88fea711b163a9b45f7b5878e44f5504d162991924958d8910c5eb7241b893ae27ea328a5efb754ba13ed0ddf7422 SHA512 fe9837a85e68e486fcc1a1903af027a71916aa70bf54d8616f5be6b13c52ca4ca7f5d2901724e3ec2e3e754c2772c59d3db78fb6e75432ef7f67e99692571bfe +AUX seaview-4.6-fno-common.patch 3171 BLAKE2B a3dfdb8d90279cdc16489d5e304eb81d3893f63d55ec5363d86fce5d90aa87c003fb2f41dafb09f46002aa1b45871161ff5b0de6e22bd24d77c98727880818d5 SHA512 89b1d46956232b6c7a3979c804339e2bc4e9f99224c7c06091a2526c92ddd55415762a39d183e0249ae7251afada28bfb6f863bd91167ea647d76d4c548c1f6a DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6 -EBUILD seaview-4.5.4.ebuild 2013 BLAKE2B 91c192d7cb22411f7af4366088c1e47c657fc75855cab2a289d4a1d7cec206302b2670612117334d6c6b79d25c578daf3da5cbd053dc98602ead9033c3b90f35 SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945 -EBUILD seaview-4.6.ebuild 1997 BLAKE2B 1c7c01e0a52f943b9506954d84519c8ff09b15d307476aa659f7bb49af9de1ea02076bb74bcebaac49a571d18624455879c321faa7458f8ac2660773eb4b8706 SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8 +EBUILD seaview-4.6-r1.ebuild 2106 BLAKE2B 6a7d4e6295285cd072db997acc3f9467fb46a813a8da640372ec55228792d85f43fce137b2c5f90d60c6e77918280192967001ad7ac6a2a80a69c390cf6ed218 SHA512 76b24794f87383ec39638569e7c61c5f500ea84a89cabb04d1bbcf101bffecc97e99729a4e29f3d4252a980c8a40889d1e4161ebea272a09946a78ecd4b75f4c MISC metadata.xml 621 BLAKE2B 9c56cc2099ed696942e2958926ee8c9f24be26fd273e74a7f789d368c3a222f084363ec3a4eada5e1197c4a81f533074f4b05c43d1e9c951e66261d55bc4d9e8 SHA512 7c49694ef56359e58b76b0dd7715d28615a541655c6ccaa2d7d64041c7340082bd5026fa2baa5a15e51e3aa27309d5a72ab836a5ee554366eb324406a50a09c4 diff --git a/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch new file mode 100644 index 000000000000..c9595748e901 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch @@ -0,0 +1,76 @@ +--- a/align.cxx ++++ b/align.cxx +@@ -754,7 +754,7 @@ + alignitems[clustalopt + MAX_MSA_ALGOS].label(strdup(options)); + alignitems[clustalopt + MAX_MSA_ALGOS].flags = attr; + if (view->alignment_algorithm < 2) alignitems[clustalopt + MAX_MSA_ALGOS + 3].flags = FL_MENU_INACTIVE; +- delete options; ++ delete[] options; + view->menu_align = alignitems; + view->menubar->add("Align", 0, NULL, (void*)view->menu_align, FL_SUBMENU_POINTER); + if (view->count_msa_algos >= MAX_MSA_ALGOS) (alignitems + clustalopt + MAX_MSA_ALGOS + 2)->deactivate(); +--- a/seaview.cxx ++++ b/seaview.cxx +@@ -3314,7 +3314,7 @@ + if(p != NULL) *p = 0; + if(printout_black == TEXT_ONLY) strcat(suggested, ".txt"); + else { +- strcat(suggested, "."PDF_OR_PS_EXT); ++ strcat(suggested, "." PDF_OR_PS_EXT); + } + if( view->alt_col_rank != NULL ) { + for(anerr = 0; anerr < view->tot_seqs; anerr++) +@@ -3424,7 +3424,7 @@ + + pdf_form = new Fl_Window(415, 90); + pdf_form->box(FL_FLAT_BOX); +-pdf_form->label("Set "PDF_OR_PS" output options"); ++pdf_form->label("Set " PDF_OR_PS " output options"); + + x = 5 + (int)fl_width("block size:"); y = 5; w = 50; h = 25; + sizeinput = new Fl_Input(x, y, w, h, "font size:"); +@@ -5000,10 +5000,10 @@ + {"Save prot alignmt", 0,file_menu_callback, 0, FL_MENU_INACTIVE}, + {"Save bootstrap replicates", 0,file_menu_callback, 0, FL_MENU_INACTIVE | FL_MENU_DIVIDER}, + #if !defined(__APPLE__) +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0}, +- {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, 0}, ++ {"" PDF_OR_PS " options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #else +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #endif + {"Concatenate", 0,file_menu_callback, 0, FL_MENU_DIVIDER}, + {"New window", FL_COMMAND | 'n', file_menu_callback, 0, 0}, +--- a/treedraw.cxx ++++ b/treedraw.cxx +@@ -210,7 +210,7 @@ + {"Save all trees", 0, file_callback, NULL, 0}, + {"Save patristic distances", 0, patristic_callback, NULL, FL_MENU_DIVIDER}, + {"Print", FL_COMMAND | 'p', file_callback, NULL, 0}, +- {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0}, ++ {"Save as " PDF_OR_PS "", 0, file_callback, NULL, 0}, + {"Save as SVG", 0, file_callback, NULL, 0}, + {"A4", 0, file_callback, NULL, FL_MENU_RADIO | 0}, + {"Letter", 0, file_callback, NULL, FL_MENU_RADIO | 0}, +--- a/xfmatpt.cxx ++++ b/xfmatpt.cxx +@@ -205,7 +205,7 @@ + compute->callback(compute_proc, fdui); + fdui->compute_butt = compute; + +-Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS); ++Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write " PDF_OR_PS); + fin += width; + postscript->callback(plot_button_proc, fdui); + +@@ -870,7 +870,7 @@ + #ifndef MICRO + matpt->form->hide(); Fl::flush(); // because of strange bug on 32-bit Linux only + #endif +- fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname()); ++ fl_message("Dot plot is now in file\n%s\nin " PDF_OR_PS " format", surface->outfname()); + delete surface; + #ifndef MICRO + matpt->form->show(); Fl::flush(); diff --git a/sci-biology/seaview/files/seaview-4.6-fno-common.patch b/sci-biology/seaview/files/seaview-4.6-fno-common.patch new file mode 100644 index 000000000000..24cc28dfb3b7 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-fno-common.patch @@ -0,0 +1,110 @@ +--- a/csrc/dnapars.c ++++ b/csrc/dnapars.c +@@ -77,41 +77,43 @@ + /* function prototypes */ + + +-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, ++extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, + weightfilename[FNMLNGTH]; + char basechar[32]="ACMGRSVTWYHKDBNO???????????????"; +-node *root; +-long chars, col, msets, ith, njumble, jumb, maxtrees; ++extern node *root; ++extern long chars, col, msets, ith, njumble, jumb; ++long maxtrees; + /* chars = number of sites in actual sequences */ +-long inseed, inseed0; +-double threshold; +-boolean jumble, usertree, thresh, weights, thorough, rearrfirst, +- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf, +- multf; ++extern long inseed, inseed0; ++extern double threshold; ++boolean thorough, rearrfirst, mulf, multf; ++extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset; + steptr oldweight; +-longer seed; +-pointarray treenode; /* pointers to all nodes in tree */ +-long *enterorder; ++extern longer seed; ++extern pointarray treenode; /* pointers to all nodes in tree */ ++extern long *enterorder; + long *zeros; + + /* local variables for Pascal maketree, propagated globally for C version: */ + +-long minwhich; ++extern long minwhich; + static double like, minsteps, bestyet, bestlike, bstlike2; +-boolean lastrearr, recompute; +-double nsteps[maxuser]; +-long **fsteps; +-node *there, *oldnufork; +-long *place; +-bestelm *bestrees; +-long *threshwt; ++extern boolean lastrearr, recompute; ++extern double nsteps[maxuser]; ++extern long **fsteps; ++extern node *there; ++node *oldnufork; ++extern long *place; ++extern bestelm *bestrees; ++extern long *threshwt; + baseptr nothing; +-gbases *garbage; +-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, ++extern gbases *garbage; ++extern node *temp, *temp1; ++node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, + *tmp2, *tmp3, *tmprm, *tmpadd; +-boolean *names; ++extern boolean *names; + node *grbg; +-char *progname; ++extern char *progname; + + + static void getoptions(int arg_maxtrees, dnapars_S_option s_option) +--- a/csrc/phylip.c ++++ b/csrc/phylip.c +@@ -35,6 +35,8 @@ + + #include "phylip.h" + ++boolean javarun; ++ + #ifdef WIN32 + #include + /* for console code (clear screen, text color settings) */ +--- a/csrc/phylip.h ++++ b/csrc/phylip.h +@@ -342,7 +342,7 @@ + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++extern boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -363,7 +363,6 @@ + extern boolean ibmpc, ansi, tranvsp; + //extern naym *nayme; /* names of species */ + extern char* *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + +--- a/csrc/protpars.c ++++ b/csrc/protpars.c +@@ -127,7 +127,7 @@ + node *temp, *temp1; + Char ch; + aas tmpa; +-char *progname; ++extern char *progname; + + /* Local variables for maketree, propagated globally for c version: */ + long minwhich; diff --git a/sci-biology/seaview/seaview-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild deleted file mode 100644 index 33ee6f65ccbd..000000000000 --- a/sci-biology/seaview/seaview-4.5.4.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils multilib toolchain-funcs - -DESCRIPTION="A graphical multiple sequence alignment editor" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="+xft" - -CDEPEND=" - sys-libs/zlib - x11-libs/fltk:1 - x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] )" -RDEPEND="${CDEPEND} - sci-biology/clustalw - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - # respect CXXFLAGS (package uses them as CFLAGS) - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "s:^CXX.*:CXX = $(tc-getCXX):" \ - -e "s:\$(OPT):${CXXFLAGS}:" \ - -e "s:^OPT:#OPT:" \ - -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ - -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ - -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ - -e "s:^USE_XFT:#USE_XFT:" \ - -e "s:^#HELPFILE:HELPFILE:" \ - -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ - -e "s:^#PHYMLNAME:PHYMLNAME:" \ - -e 's:-lXinerama::g' \ - -e 's:-lpng::g' \ - -e 's:-ljpeg::g' \ - -e 's:-lfontconfig::g' \ - -i Makefile || die "sed failed while editing Makefile" - - if use xft; then - sed \ - -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ - -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ - -i Makefile || die "sed failed while editing Makefile to enable xft" - else - sed -i -e "s:-lXft::" Makefile || die - fi -} - -src_install() { - dobin seaview - - # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile - insinto /usr/share/seaview - doins example.nxs seaview.html - - insinto /usr/share/seaview/images - doins seaview.xpm - - make_desktop_entry seaview Seaview - - doman seaview.1 -} diff --git a/sci-biology/seaview/seaview-4.6-r1.ebuild b/sci-biology/seaview/seaview-4.6-r1.ebuild new file mode 100644 index 000000000000..469f88728120 --- /dev/null +++ b/sci-biology/seaview/seaview-4.6-r1.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit desktop toolchain-funcs + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+xft" + +RDEPEND=" + sci-biology/clustalw:2 + sci-biology/phyml + || ( + sci-libs/libmuscle + sci-biology/muscle + ) + sys-libs/zlib + x11-libs/fltk:1[xft?] + x11-libs/libX11 + xft? ( x11-libs/libXft )" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +S="${WORKDIR}/${PN}" +PATCHES=( + "${FILESDIR}"/${PN}-4.6-fno-common.patch + "${FILESDIR}"/${PN}-4.6-Wreserved-user-defined-literal.patch +) + +src_prepare() { + default + + # respect CXXFLAGS (package uses them as CFLAGS) + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "s:^CXX.*:CXX = $(tc-getCXX):" \ + -e "s:\$(OPT):${CXXFLAGS}:" \ + -e "s:^OPT:#OPT:" \ + -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ + -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ + -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ + -e "s:^USE_XFT:#USE_XFT:" \ + -e "s:^#HELPFILE:HELPFILE:" \ + -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ + -e "s:^#PHYMLNAME:PHYMLNAME:" \ + -e 's:-lXinerama::g' \ + -e 's:-lpng::g' \ + -e 's:-ljpeg::g' \ + -e 's:-lfontconfig::g' \ + -i Makefile || die "sed failed while editing Makefile" + + if use xft; then + sed \ + -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ + -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ + -i Makefile || die "sed failed while editing Makefile to enable xft" + else + sed -i -e "s:-lXft::" Makefile || die + fi +} + +src_install() { + dobin seaview + + # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile + insinto /usr/share/seaview + doins example.nxs seaview.html + + insinto /usr/share/seaview/images + doins seaview.xpm + + make_desktop_entry seaview Seaview + + doman seaview.1 +} diff --git a/sci-biology/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6.ebuild deleted file mode 100644 index 4ad8ad61b72b..000000000000 --- a/sci-biology/seaview/seaview-4.6.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils toolchain-funcs - -DESCRIPTION="A graphical multiple sequence alignment editor" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="+xft" - -RDEPEND=" - sys-libs/zlib - x11-libs/fltk:1 - x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] ) - sci-biology/clustalw:2 - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - default - - # respect CXXFLAGS (package uses them as CFLAGS) - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "s:^CXX.*:CXX = $(tc-getCXX):" \ - -e "s:\$(OPT):${CXXFLAGS}:" \ - -e "s:^OPT:#OPT:" \ - -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ - -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ - -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ - -e "s:^USE_XFT:#USE_XFT:" \ - -e "s:^#HELPFILE:HELPFILE:" \ - -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ - -e "s:^#PHYMLNAME:PHYMLNAME:" \ - -e 's:-lXinerama::g' \ - -e 's:-lpng::g' \ - -e 's:-ljpeg::g' \ - -e 's:-lfontconfig::g' \ - -i Makefile || die "sed failed while editing Makefile" - - if use xft; then - sed \ - -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ - -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ - -i Makefile || die "sed failed while editing Makefile to enable xft" - else - sed -i -e "s:-lXft::" Makefile || die - fi -} - -src_install() { - dobin seaview - - # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile - insinto /usr/share/seaview - doins example.nxs seaview.html - - insinto /usr/share/seaview/images - doins seaview.xpm - - make_desktop_entry seaview Seaview - - doman seaview.1 -} diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest deleted file mode 100644 index 6a5d38227ddb..000000000000 --- a/sci-biology/shrimp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 -EBUILD shrimp-2.2.3.ebuild 1818 BLAKE2B 4878f0ce5782f0bc5fb5d4b14d5d713f21268b612cb18a2f14e19e3cca1c2270940b1f74220da0788fea9e142c803bcc77b9b2c04479a9432f06b9b29f3f7705 SHA512 2bfdb6f1cf7678dc9fafd66c25c07f55671f39600a44c606bac33652806105ff448d231202fb405307a0a49716557aa7cc63d371163821af2d919422ff9e2e6f -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/shrimp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild deleted file mode 100644 index 2b57b032a1b2..000000000000 --- a/sci-biology/shrimp/shrimp-2.2.3.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit flag-o-matic python-single-r1 toolchain-funcs - -MY_PV=${PV//./_} - -DESCRIPTION="SHort Read Mapping Package" -HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" -SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" - -LICENSE="shrimp" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="custom-cflags +cpu_flags_x86_sse2" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# file collision on /usr/bin/utils #453044 -DEPEND="!sci-mathematics/cado-nfs" -RDEPEND="${DEPEND} - ${PYTHON_DEPS}" - -S=${WORKDIR}/SHRiMP_${MY_PV} - -pkg_pretend() { - use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" -} - -pkg_setup() { - if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then - elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" - die "C compiler lacks OPENMP support" - fi - python-single-r1_pkg_setup -} - -src_prepare() { - sed \ - -e '1 a #include ' \ - -i common/dag_glue.cpp || die - # respect LDFLAGS wrt 331823 - sed \ - -e "s/LDFLAGS/LIBS/" \ - -e "s/\$(LD)/& \$(LDFLAGS)/" \ - -e 's/-static//' \ - -i Makefile || die - - append-flags -fopenmp - if ! use custom-cflags; then - append-flags -O3 - replace-flags -O* -O3 - fi - tc-export CXX - - cd utils || die - sed -e '/^#!/d' -i *py || die - sed -e '1i#!/usr/bin/python' -i *py || die -} - -src_compile() { - emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -} - -src_install() { - local i - newdoc bin/README README.bin && rm bin/README - dobin bin/* utils/split-contigs utils/temp-sink - dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES - - pushd utils > /dev/null - - python_doscript *py - - rm *.py *.o *.c split-contigs temp-sink || die - insinto /usr/share/${PN} - doins -r * -} diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest index 5c5b222e5a61..818622d6ba58 100644 --- a/sci-biology/unafold/Manifest +++ b/sci-biology/unafold/Manifest @@ -1,3 +1,4 @@ +AUX unafold-3.8-doc-version.patch 308 BLAKE2B 6fba108c6338f9b974fc20e328f9af7d4ffc735889a32b74e36573ed68453af11922c15c626c48b997784378ad9cec79fe928ef184a224bcca570c7d59158851 SHA512 53a7ad53704830ac50fa463fb340cd8823e57af83b97ee40a969a338af62bce11934bc54b37a43b4f5bdd4faea919b2e3b4d8532926a8c185f53dcb5ce3c5afd DIST unafold-3.8.tar.bz2 282418 BLAKE2B 0dddff9dc440362ce3b24d18f42aa47d2dc817de93eba900de76dc73393feabb09ac57cb77af6c8db0ab8c0958f0fd459911fd813fa004b616fedffe9aebd069 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c -EBUILD unafold-3.8-r1.ebuild 589 BLAKE2B 345d178e5bdec00c1a6420b6b4d6598ffcb49474bd756b8a6dd50406fb1718969debeeeb27a2a804c53b6c518583e12499a0ca99d136b2bb47ffa559a87bd7e9 SHA512 4b025f8e4b52ef5e833d299973d44e5846000c45b7f36f200dc14414cb1367188f228e8fba23782f19475a38eb6f6d1cf8ca053b5d70f8b573aee69da7fc71b9 +EBUILD unafold-3.8-r1.ebuild 609 BLAKE2B 4f6e5867e63d272781eb88b6cfef00e41a067b7e97a8c61ee0e5c380369e155452afa6c35f153a3b3c39ea54cd02c2ed039ea793fb0f52b7afc91bf45e2c8ca4 SHA512 3ffe39a79f0162a645237cc5c4763abd0b41775f09546d2cf792ed9dcfe30219ba9540feac3ae8758616c5f0f48de3b7643b17d6682cf426a8f9f799e509b9e1 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/unafold/files/unafold-3.8-doc-version.patch b/sci-biology/unafold/files/unafold-3.8-doc-version.patch new file mode 100644 index 000000000000..b15858fd69e6 --- /dev/null +++ b/sci-biology/unafold/files/unafold-3.8-doc-version.patch @@ -0,0 +1,11 @@ +--- a/tests/hybrid.tml ++++ b/tests/hybrid.tml +@@ -10,7 +10,7 @@ + + + +- hybrid (UNAFold) 3.7 ++ hybrid (UNAFold) 3.8 + By Nicholas R. Markham and Michael Zuker + Copyright (C) 2006 + Rensselaer Polytechnic Institute diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild index e4fff4e8cabd..6aec75f0336d 100644 --- a/sci-biology/unafold/unafold-3.8-r1.ebuild +++ b/sci-biology/unafold/unafold-3.8-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 inherit flag-o-matic @@ -14,14 +14,17 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="custom-cflags" -DEPEND="" -RDEPEND="${DEPEND}" +RDEPEND=" + media-libs/freeglut + media-libs/gd + virtual/opengl" +DEPEND="${RDEPEND}" -src_prepare() { +PATCHES=( "${FILESDIR}"/${P}-doc-version.patch ) + +src_configure() { # recommended in README use custom-cflags || append-flags -O3 - sed \ - -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \ - -i tests/hybrid.tml || die + default } diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest deleted file mode 100644 index 0de0a4ebedfe..000000000000 --- a/sci-biology/vienna-rna/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -AUX vienna-rna-2.1.1-impl-decl.patch 354 BLAKE2B d9d7a4e749a2c8681dc619961291f5e082681f15729a72ee1423bc4af71e8f745a558506e7147846c84df8fb7e5d316d1bc253f8125487a4ea6aab3c05b19bd8 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b -AUX vienna-rna-2.1.1-prll.patch 885 BLAKE2B 168d4b1a4c5ff0eb92379fe5762e7f0d6b7676c774c659422923c894bfcdb9efbbe20979ed87129c688b6ced9ad19cc51716164a0056b19fbc80fc27bbd32d57 SHA512 1b80636b43e1ce9ca54431358b45f2503ef3f49b8cd049b5ef501058e1771bda3628c88e63cc1bea9a32aff5a004ccef663b47dae385a5df6071793f292dff94 -AUX vienna-rna-2.1.8-bindir.patch 367 BLAKE2B 9bf3df6c604d5ac0661188d4f662ee12387f8bb30c2e3ecbd4a7bfd0a73ff5419f7a10b2fe70efd53e4b634bfdd3c1039ec000b26e7f5edbbcc4242a4edf5914 SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf -DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e -EBUILD vienna-rna-2.1.8.ebuild 2588 BLAKE2B 5a1692be0a587cc85dcf0a60c609ff0c4eade92e5da98ce05bf2d90a195e606d9ca9262774c2c6875b1d9d53451b5043d7c4ae8a3446d4ebf3607effe039cd92 SHA512 4474f2bf042a31e02fd7b9882f6b5ec17fef4ba9f23eab29a39e9c09ea29414e836c029e568a905a2c315370c763384f9d84547a56a8806216dc825d51c3d378 -MISC metadata.xml 1324 BLAKE2B ba9d5e1f5893344fd1899e3723e1b86bac75546cde97b311fe7ef9dc2068f1a063cd5a5d2ac65d1195f532441194e8943ad2ec44db9a5c614ed0c8d894a900bb SHA512 8198db695aea5244b62fab23fd0a53a0657f8d37cc741f60869a39374e97c725b564086d852e37216c584083168881eba246f59b840d6a41bfe9246d3bd88d4b diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch deleted file mode 100644 index de457f318e8e..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch +++ /dev/null @@ -1,15 +0,0 @@ - Readseq/readseq.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/Readseq/readseq.c b/Readseq/readseq.c -index 8af7b39..56a25ae 100644 ---- a/Readseq/readseq.c -+++ b/Readseq/readseq.c -@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' - #include - #include - #include -+#include - - #include "ureadseq.h" - diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch deleted file mode 100644 index ee4aef5c3308..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch +++ /dev/null @@ -1,30 +0,0 @@ - Readseq/Makefile | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Readseq/Makefile b/Readseq/Makefile -index f073aaa..05f2edd 100644 ---- a/Readseq/Makefile -+++ b/Readseq/Makefile -@@ -6,11 +6,11 @@ - # - - # pick an ANSI C compiler (the default Sun CC is not ANSI) --CC=gcc # Gnu C Compiler -+CC?=gcc # Gnu C Compiler - #CC=cc # SGI Irix - #CC=vcc # some DEC Ultrix - --CFLAGS= -+CFLAGS?= - #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum - # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software - -@@ -40,7 +40,7 @@ all: build test - - build: $(SOURCES) - @echo "Compiling readseq..." -- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c -+ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c - - # if using NCBI, uncomment these lines in place of build: above - #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch deleted file mode 100644 index e54dff95b485..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/Utils/Makefile.am b/Utils/Makefile.am -index f42ebf4..d84a0f1 100644 ---- a/Utils/Makefile.am -+++ b/Utils/Makefile.am -@@ -1,4 +1,4 @@ --pkgbindir = $(pkgdatadir)/bin -+pkgbindir = $(prefix)/bin - pkgbin_PROGRAMS = b2ct popt ct2db - - pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml deleted file mode 100644 index bbc3d41fb4a6..000000000000 --- a/sci-biology/vienna-rna/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - The Vienna RNA Package consists of a C code library and several - stand-alone programs for the prediction and comparison of RNA secondary - structures. RNA secondary structure prediction through energy - minimization is the most used function in the package. We provide three - kinds of dynamic programming algorithms for structure prediction: the - minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a - single optimal structure, the partition function algorithm of - (McCaskill 1990) which calculates base pair probabilities in the - thermodynamic ensemble, and the suboptimal folding algorithm of - (Wuchty et.al 1999) which generates all suboptimal structures within a - given energy range of the optimal energy. For secondary structure - comparison, the package contains several measures of distance - (dissimilarities) using either string alignment or tree-editing - (Shapiro and Zhang 1990). Finally, we provide an algorithm to design - sequences with a predefined structure (inverse folding). - - diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild deleted file mode 100644 index 7664f6d3dc6e..000000000000 --- a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_OPTIONAL=true -AUTOTOOLS_AUTORECONF=true -AUTOTOOLS_IN_SOURCE_BUILD=1 - -inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs - -DESCRIPTION="RNA secondary structure prediction and comparison" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" -SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz" - -SLOT="0" -LICENSE="vienna-rna" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="doc openmp python static-libs" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-lang/perl - media-libs/gd - doc? ( dev-texlive/texlive-latex ) - python? ( ${PYTHON_DEPS} )" -DEPEND="${RDEPEND} - python? ( dev-lang/swig:0 )" - -S="${WORKDIR}/ViennaRNA-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-bindir.patch - "${FILESDIR}"/${PN}-2.1.1-prll.patch - "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch -) - -src_prepare() { - sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die - sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die - - autotools-utils_src_prepare - - if use python; then - cd interfaces/Python || die - local PATCHES=() - distutils-r1_src_prepare - fi -} - -src_configure() { - local myeconfargs=( - --with-cluster - $(use_enable openmp) - ) - - use doc || \ - myeconfargs+=( - --without-doc-pdf - --without-doc-html - --without-doc - ) - autotools-utils_src_configure - sed \ - -e "s:CC=gcc:CC=$(tc-getCC):" \ - -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ - -i Readseq/Makefile || die - if use python; then - cd interfaces/Python || die - distutils-r1_src_configure - fi -} - -src_compile() { - autotools-utils_src_compile - autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) - - # TODO: Add (optional?) support for the NCBI toolkit. - if use python; then - cd interfaces/Python || die - emake RNA_wrap.c - distutils-r1_src_compile - fi -} - -src_test() { - autotools-utils_src_compile -C interfaces/Perl check - use python && autotools-utils_src_compile -C interfaces/Python check - autotools-utils_src_compile -C Readseq test -} - -src_install() { - autotools-utils_src_install - - if ! use static-libs; then - rm -f "${ED}"/usr/$(get_libdir)/*.a || die - fi - - newbin Readseq/readseq readseq-vienna - dodoc Readseq/Readseq.help - newdoc Readseq/Readme README.readseq - newdoc Readseq/Formats Formats.readseq - - # remove perlocal.pod to avoid file collisions (see #240358) - perl_delete_localpod || die "Failed to remove perlocal.pod" - if use python; then - cd interfaces/Python || die - distutils-r1_src_install - fi -} -- cgit v1.2.3