diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2020-06-29 11:38:31 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2020-06-29 11:38:31 +0100 |
| commit | 90c88731bd036e5698b281fbc0a5f3aa4c9983ac (patch) | |
| tree | 83fc5facb6b12be510a37bc3d241cc63e965b13a /sci-biology | |
| parent | feb0daf81d888e9160f9f94502de09b66f2a63fd (diff) | |
gentoo resync : 29.06.2020
Diffstat (limited to 'sci-biology')
24 files changed, 366 insertions, 321 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 81993963acb7..e6da050cedc7 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index b482298f23a1..bc1d45a744ea 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,4 +1,4 @@ AUX abyss-2.0.3-prog-AR.patch 350 BLAKE2B 20e1a428ea02c3c67c5df9b92f623ddea58f2054912d0ca788f0a9890057277cd98babe48d089852541db262ab0a69e95ead2a4b31456a62597ae1d4856e8c5e SHA512 747e9d258767c698a95615ae83db18662ec1851c0a6dfcdcec6aea68dc76415e89b3f85f1f8ff6c04fff22052c787a43948f8f3588220e2dc66cc7262788c52a DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 -EBUILD abyss-2.0.3-r1.ebuild 1555 BLAKE2B 113efb423e315a0b4abf19b8a75326a90f8da5b88db1d0a5bd5485d6eead927dc7b72398452a0794edf5ec9a2c0dffabf6fe4f15aaa66f48c7cc5e2ca9615c29 SHA512 0ec8921c93ad555f35135f707ae4b71f1e0640e82d81e96a966df755313463c8ddf68991e7602435d5d762ddda8ec5ebc4763bed674985b5cd2cfaefc729a744 +EBUILD abyss-2.0.3-r2.ebuild 1556 BLAKE2B a25f93323564ce83b2a15ed31881a873ddafe688f9277439aef25dbb3a76c6d796984105498c2f547bf00229ce4c465d9e5c22c949c543b29fd61c22a8d52568 SHA512 9c5649115d97c8b6aee3909d092f8429c59c31b9200b71023bb05e3bc2501c3f55a1d4b07c9bacbfd94fc6a10a4a5124a6135b743e29d126856796bab5ea1f3f MISC metadata.xml 572 BLAKE2B 987284bc0e435174f2592854cf67e44d155b64975a65d69fc988352f9bf0c06bfa412bcbba0e3a5a4819a846d5fd1c5695627b8b75ab7c955abff1b0bb4ad76e SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198 diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild index 800a45964cd0..b9aed09d3eec 100644 --- a/sci-biology/abyss/abyss-2.0.3-r1.ebuild +++ b/sci-biology/abyss/abyss-2.0.3-r2.ebuild @@ -19,7 +19,7 @@ RDEPEND=" dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= - virtual/libffi:0= + dev-libs/libffi:0= ) mpi? ( sys-cluster/openmpi )" DEPEND="${RDEPEND} diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest index a83edfa3624a..54dff0d8887c 100644 --- a/sci-biology/infernal/Manifest +++ b/sci-biology/infernal/Manifest @@ -1,8 +1,6 @@ -AUX infernal-1.0.2-ldflags.patch 444 BLAKE2B 287cac3afc2898d51e5dbf82b64e793dc5decfa134365e91f1ea599df63ca736ec979063a64f2ff3a52bd5213a836a0f2b9875b5142c4a8245403261d5b382b1 SHA512 95f953bbf57a78f40df51bbfdab62e715905aa2bc57d4ca75e380c81d34c88d0177e6fe51933c908bf6e6f513b8c38ffeeb7c8f1802773c7c9773a36388b81d0 +AUX infernal-1.0.2-fix-build-system.patch 3142 BLAKE2B e5869c089b158cb8c22bff849e2a6c22a01d485f53b0da61c662cac51bb04e3cbfb2a8af9c71ac225760676f20db2f34c12fb674eac71ab995c3dbcfc7d9658e SHA512 4013676d6e79075fc0d31aa73effbdff8d391c122e5d168c93ed007c24f555a5f8c5e225461d074855b814e2c7d19ef1b804c3d82e5e5c018259e2907f2e168e AUX infernal-1.0.2-overflows.patch 540 BLAKE2B 1336442c3d1ef8a78d5d7a345bbbc3abf918d6edb0cef8fddcac32b9ece9f990464b3815592f564a05494a8b7c5c75e438349c384c29caa73c467e40f737db45 SHA512 c8bafb2c10d09cae24f882d5238b6ae974669d59e0ee583bcedb13e81c88ea9859c1f78343d5be91a5cca05a3dc07ffe6436b33e201a46baf349795da5eec906 -AUX infernal-1.0.2-parallel-build.patch 659 BLAKE2B ab11ef5e62268818d9cf4a871c82931ac85c564c3990fc06a4f74d8f826f4bda16150bde790681ac416ba40e0fc2cef9331942d30b25249a11a58434d56935e6 SHA512 d67271d858f60a5378d61892cd5c354ac95234620437621f3bf770e8829fa866a451ee031f530f502385044d7622f0fe88827614e95ab35ac6cbf8384d21e9c5 AUX infernal-1.0.2-perl-5.16-2.patch 4206 BLAKE2B eb4309d31e874f395d20bded4c132fb8b811fe17b4af5c95bd56ade05e22e7bf45c08e67884ca339aa7a2e13b2ddc9bb9527cbddef9458ce8fe05b7bd4707e49 SHA512 9784f31c18f6c53b15c0454d3a41db27c3f433ac3d3030bc113e9f9e8194fb51109de5055d038a3c639b1c4142d6fd0010825df484a857c9f072f43d8cadcb44 -AUX infernal-1.0.2-respect-DESTDIR.patch 396 BLAKE2B 822a6c543c0ad0a0ff75cc3fd50c4bbb84791cadcd4a93ad1a498b7464562dd00eea7424324f1bf715802c0dc9824dced0d16bd76d65ba9b7886b536b32fb988 SHA512 6847c87e45a34a68d179fbf8c9965af502cc9e52aa1f5ed800332dfb52e97ca3f2cb87a7dc4c3adb2d85f63567f15b084a50c7139f5ab03b0cf2b0711d023ec4 DIST infernal-1.0.2.tar.gz 15205421 BLAKE2B 3570ae42feb96ead383c2f1c09d34b4719ae0a5ae8fa973fd02f9ea6e8935c81ab49c7db21dad2e20c1ae6ab6fb9514f12704bbf5917f15f6582effae480312f SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af -EBUILD infernal-1.0.2-r1.ebuild 924 BLAKE2B 8a1af66f6ea82e8232d052d5361384a1082569344bf642b3e29b6f2d46dd1889c5780f3617e4d514857da013ec117e55cefa135aeb58587217746902da81b139 SHA512 816308be6a7e57e30f7c22e0c37662cde9b234501e324889e7e21e4d0e779cc6bb113490f10ce1aba3aeff46bdf9668442878e3cea4d5ad171beeb0e9fe6832c +EBUILD infernal-1.0.2-r1.ebuild 886 BLAKE2B 8f82a57ed31081abb50ee798ad80f3de5b7db8dbc3a3428b150de486834fae52253d9765d27a19276cbd79daf9a522c52733caf7a1ed824064932dbae3ade282 SHA512 af5e2dd5822150faa278e4160e41696a322deec3ac97e3df0cc100a1b8cebc929c747235a051ac86afed0269812f10dfb005160a56b49703aa67376064c49ad1 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..41ab3103594b --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch @@ -0,0 +1,135 @@ +* Fix parallel build +* Respect AR +* Respect DESTDIR +* Respect LDFLAGS + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -17,7 +17,6 @@ + # + CC = @CC@ + CFLAGS = @CFLAGS@ +-AR = @AR@ rcv + LN = ln + RANLIB = @RANLIB@ + LDFLAGS = -static @LDFLAGS@ +@@ -132,13 +131,13 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< + + libeasel.a: $(OBJS) +- $(AR) libeasel.a $(OBJS) ++ $(AR) rcv libeasel.a $(OBJS) + $(RANLIB) libeasel.a + chmod 644 libeasel.a + +--- a/easel/testsuite/Makefile.in ++++ b/easel/testsuite/Makefile.in +@@ -15,7 +15,6 @@ + LIBS = @LIBGSL@ @LIBS@ -lm + MPILIBS = @MPILIBS@ + +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + ESLDIR = .. +--- a/iinfernal-1/Makefile.in ++++ b/iinfernal-1/Makefile.in +@@ -20,7 +20,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libhmmer.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + MPILIBS = @MPILIBS@ +@@ -63,7 +62,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + +--- a/Makefile.in ++++ b/Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +@@ -202,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ +--- a/rigfilters/cfsqp/Makefile.in ++++ b/rigfilters/cfsqp/Makefile.in +@@ -24,7 +24,6 @@ + ## archiving command, and ranlib command. + # these are used to create the libcfsqp.a library, necessary for cm2hmm + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + OBJS = cfsqp.o\ +@@ -41,7 +40,7 @@ + all: libcfsqp.a + + libcfsqp.a: $(OBJS) ${HDRS} +- $(AR) libcfsqp.a $(OBJS) ++ $(AR) rcv libcfsqp.a $(OBJS) + $(RANLIB) libcfsqp.a + chmod 644 libcfsqp.a + +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -27,7 +27,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libinfernal.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + # configuration for optional MPI functionality +@@ -86,7 +85,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# +@@ -95,7 +94,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) ${HDRS} +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch deleted file mode 100644 index f688dce152ed..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch +++ /dev/null @@ -1,15 +0,0 @@ -Respect LDFLAGS - -http://bugs.gentoo.org/show_bug.cgi?id=338177 - ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -86,7 +86,7 @@ - all: $(PROGS) - - $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} -- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) -+ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) - - - ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch deleted file mode 100644 index 67ffa6fda7f6..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix parallel build - -http://bugs.gentoo.org/show_bug.cgi?id=311919 - ---- a/Makefile.in -+++ b/Makefile.in -@@ -82,9 +82,10 @@ - all: core - - core: -- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) -- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) -- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") -+ $(MAKE) -C easel -+ $(MAKE) -C src -+ $(MAKE) -C src module -+ $(MAKE) -C testsuite - - #.PHONY: $(RIGFILTERS) - #$(RIGFILTERS): core ---- a/easel/Makefile.in -+++ b/easel/Makefile.in -@@ -132,7 +132,7 @@ - esl_wuss.o - - all: libeasel.a -- (cd miniapps; make) -+ $(MAKE) -C miniapps - - .c.o: - ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch deleted file mode 100644 index ea465e592ffa..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch +++ /dev/null @@ -1,16 +0,0 @@ -Build system does not respect DESTDIR by default. - ---- a/Makefile.in -+++ b/Makefile.in -@@ -203,9 +203,9 @@ - # "make install" installs the programs in BINDIR - # - install: -- mkdir -p ${BINDIR} -+ mkdir -p $(DESTDIR)${BINDIR} - for file in $(PROGS); do\ -- cp src/$$file $(BINDIR)/;\ -+ cp src/$$file $(DESTDIR)$(BINDIR)/;\ - done - # if test -d $(RIGFILTERS); then\ - # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index e906c23024ff..2e96418b6bb9 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 + +inherit toolchain-funcs DESCRIPTION="Inference of RNA alignments" HOMEPAGE="http://infernal.janelia.org/" @@ -9,21 +11,20 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -IUSE="mpi" KEYWORDS="amd64 x86" +IUSE="mpi" RDEPEND="mpi? ( virtual/mpi )" DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-overflows.patch "${FILESDIR}"/${P}-perl-5.16-2.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-respect-DESTDIR.patch ) src_configure() { + tc-export AR econf $(use_enable mpi) } diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest index 8bef0282bc82..39003fd43076 100644 --- a/sci-biology/mcl/Manifest +++ b/sci-biology/mcl/Manifest @@ -1,4 +1,5 @@ -AUX mcl-14.137-qa-implicit-declarations.patch 786 BLAKE2B c7a5ed8f32dd3542766beaed19c9236a137444fdf69252becedfcc2d97136b0eba276355d2b24a38a06e0f78e6eaeb813bdc713cb01161167d4a2c65425e3c03 SHA512 e1388441e06075e951a1ff9994a8e9fe1083042c09e072c68e9abb20dc4a83498eb4cb71aa71d738268a50a0e03ee8e7976df9bbb304b8c90314d682bb8625d3 +AUX mcl-14.137-fix-autotools.patch 1524 BLAKE2B baad5d167379b8f38543159d88f66367bc625e53f457a59dfbbddadd998423d924afdff6d826c6c35004e1f4a83bbbb464d3bfe367f3257adcd6fad5cd2d5aad SHA512 bb7384d8f5a819fa1e0af7bdc5b7ef157f76c1ddb3bcc5d9bca06347b5bd86d977d9580e99161e173fef8aee288ec1075d19ab9878782fa1d97eca50bae099de +AUX mcl-14.137-fix-declarations.patch 1266 BLAKE2B 2df8acbe98dfbf804b81950e1d60963fea49aeff0b8bce52c75bb757d72cb16adbf13b8567acb8b63ab76af63da3086fdedf25d363f2986881bb70e2b27630b9 SHA512 cce0825fe7d01a3f6c69bf1d1fcac1277b3beef6cca0f3ee729d2c4f60f57ef2a9223b7f3a8f63743011751790c625ec3601cc46fddde236eef37cbce982a9d6 DIST mcl-14-137.tar.gz 3035491 BLAKE2B d6b975841a9094055306056ae0cd646cc92af69018893981d32b0604a583f61d3764bc67c1e21a0861b89a17013c01bcd4c1d7cbb4e0c5856403c2a767121423 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 -EBUILD mcl-14.137.ebuild 651 BLAKE2B 73ba9d5ac8159a10ced22a9a39e0d5c1c4943fe5cc4ad1e823592e6362ef1f9bd3f850173a6e2c91d43bcfb825d3fd4de91dad469b27e58bd2a43c036889415f SHA512 042277297965d4796d0805dad2a951e8bd467630c7904fe1a5211616fc2a620c041ea6093bbaf10e6fed17037bccd7013afcfb0260e69c09bd1cdc3ca2f76f53 +EBUILD mcl-14.137.ebuild 569 BLAKE2B 0fae322e4911c52407d9b053dfcb1d08dc19624c1b32e68800135338b44e16d82eee4f77f1b11b88f002c5739b2f01c356d21154c48fe305800b88d802febaa0 SHA512 1be49c6038260326f6fe64bf0afba78258d355e8e74f3f3cfc30dd1f0de2971159ac3fb969b09710df8eeb28fa559135516189d9e56544287fd2089a572b68e3 MISC metadata.xml 336 BLAKE2B 077cf6e56ca5ba6480b00411536b1814f73b8dc93faf9337e0e81f3c47f174172894487ef072637dd396f39a95cd3a6538c2fd3e62328c3659882629c9b96dff SHA512 41ed664e2fdc26c5984fb55d90365cb02fe0de893d74e74935d2a9f6eb17e2e56a33210ed7d03c28375fb27ebbae3dca472de79a2e387ecf769a604aea629da3 diff --git a/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch new file mode 100644 index 000000000000..0d2c052a91b0 --- /dev/null +++ b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch @@ -0,0 +1,52 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -144,6 +144,7 @@ + AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_RANLIB ++AM_PROG_AR + + # Checks for libraries. + # FIXME: Replace `main' with a function in `-lm': +--- a/doc/Makefile.am ++++ b/doc/Makefile.am +@@ -9,7 +9,6 @@ + ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org> + TIDY = tidy + +-docdir = $(datadir)/doc/$(PACKAGE) + + # mclfamily.html mclfamily.ps + +--- a/graphs/Makefile.am ++++ b/graphs/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $ + +-exampledir = $(datadir)/doc/$(PACKAGE)/examples ++exampledir = $(docdir)/examples + + example_DATA = falkner.mci falkner2.mci falkner.coords make-falkner.pl \ + proteins.mci matula.mci lattice.mci honey.mci seven.mci infinity.mci \ +--- a/img/Makefile.am ++++ b/img/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $ + +-exampledir = $(datadir)/doc/$(PACKAGE)/examples ++exampledir = $(docdir)/examples + + example_DATA = fa_1024.png fa_400.png fa_600.png fa_large.png fa.ps falkner-bidi.ps falkner.ps small.ps small.png + +--- a/src/alien/oxygen/doc/Makefile.am ++++ b/src/alien/oxygen/doc/Makefile.am +@@ -17,7 +17,6 @@ + ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org> + TIDY = tidy + +-docdir = $(datadir)/doc/$(PACKAGE) + + ## zoemtut.html is "on hold": do not install; zoem is not yet ready + ## for prime time diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch index df4309874d48..4974d352bf7b 100644 --- a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch +++ b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch @@ -5,8 +5,34 @@ Fix QA issues related to implicit declarations. * clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration] * mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration] ---- mcl-14-137/src/shcl/clmadjust.c -+++ mcl-14-137/src/shcl/clmadjust.c +--- a/src/impala/iface.h ++++ b/src/impala/iface.h +@@ -16,15 +16,15 @@ + + /* This file currently provides nothing */ + +-dim nu_meet_can ; +-dim nu_meet_sl ; +-dim nu_meet_zip ; +-dim nu_diff_can ; +-dim nu_diff_sl ; +-dim nu_diff_zip ; +-double nu_magic ; ++extern dim nu_meet_can ; ++extern dim nu_meet_sl ; ++extern dim nu_meet_zip ; ++extern dim nu_diff_can ; ++extern dim nu_diff_sl ; ++extern dim nu_diff_zip ; ++extern double nu_magic ; + +-dim mclx_n_thread_g ; ++extern dim mclx_n_thread_g ; + + #endif + +--- a/src/shcl/clmadjust.c ++++ b/src/shcl/clmadjust.c @@ -14,6 +14,7 @@ #include "report.h" #include "clmadjust.h" @@ -15,8 +41,8 @@ Fix QA issues related to implicit declarations. #include "util/io.h" #include "util/types.h" #include "util/err.h" ---- mcl-14-137/src/shmcx/mcxi.c -+++ mcl-14-137/src/shmcx/mcxi.c +--- a/src/shmcx/mcxi.c ++++ b/src/shmcx/mcxi.c @@ -8,6 +8,7 @@ */ diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild index e48198deca29..e7924bccec30 100644 --- a/sci-biology/mcl/mcl-14.137.ebuild +++ b/sci-biology/mcl/mcl-14.137.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit autotools @@ -16,16 +16,14 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="+blast" -PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch") S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${P}-fix-declarations.patch + "${FILESDIR}"/${P}-fix-autotools.patch +) + src_prepare() { - find \ - -name Makefile.am \ - -exec sed \ - -e '/docdir/d' \ - -e '/exampledir/s:doc::g' \ - -i '{}' + || die default eautoreconf } diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest index c7e6e27a6c45..7b85951ec539 100644 --- a/sci-biology/poa/Manifest +++ b/sci-biology/poa/Manifest @@ -1,4 +1,5 @@ -AUX 2-respect-flags.patch 743 BLAKE2B f4da40ae90b7304520232cc9c2d61a3eecaac6ba1b9b886b29e473b1df8766286e3fd89874e2e836b9ddcd91f4bffe276ad74c1b6d073af3c1ca91e540f96c30 SHA512 496415d501040057155ba2ba261564fc00dc764626c8d41081f5463b0b40f9eae978bb8a81db15cf90f193c4ca9fe8725a2876ed175e15d37a983196b70e192f +AUX poa-2-fno-common.patch 357 BLAKE2B 5d239201e987f1fc45e82019a27b2c8e81015cd2b6b5b35f90838a8fff16bb08b51da5e6e9e1ac163bd6591341ba96a870fce4949a79e9ca558ce8c765d15ba4 SHA512 9d8f6552fd43a0f40da9cb7a5316e0e434df793fb9f7522b60e067061d14a7b27299feb02a8603cb4f6039b205723f562ea5c54c15ab3bd6582f2e6e7c223c43 +AUX poa-2-respect-flags.patch 874 BLAKE2B ee278cdbc6ec0603bc28087bd008caa70fe39668360a1473891ed997bde93f31ef7586acc9137a23a4d3123047ce5b600c3d6418a89e1e62ca70545b99a3112b SHA512 95e2e7c43ba18f9238b379ea13d3a6004cf580c75d484dbe43f01c823484f84eb93c3d2fe1ae3c98583c51c660ab24e6dc580d132649adedbf30d8675d8107b0 DIST poaV2.tar.gz 62612 BLAKE2B 92f7b2926dd7fc93745411fc04c8dd3380c32e3e87cf89afa81aefe787a1aa0e7a416d08809cce531a21d5118398a9474a751a742ee1fca47e83bd907444e9c0 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c -EBUILD poa-2-r1.ebuild 945 BLAKE2B 73d50cff0c550fe82490c93ca07db3661a71a0a2d6f67ad2d69fe658f156734aba5702137adae5cf091ff9e1e6f153894259ecfaabed05be92858038c7042668 SHA512 2c76bd5587239e7f260aeb82c362008610904dda01907a224577af9e0ef06cad8012ff21788edc24d7d3ae360867748b5e245fc73b6e1480f890787cea727c66 +EBUILD poa-2-r1.ebuild 857 BLAKE2B 436c6a4db2fa826ebb3f0a3d59df5d88f746a6c025f227be6b4916f7b6b34dde51013ae48355ea080dc19ba763972e62d3b1a87b17c19349ba0f3ed2df50409c SHA512 7fadf68dd86ac01c83eb65ef6e8512428b7c5fa84b1071f538458e46ff3116d02ff4f18a7d8e2bc32c360caee2bac2ca998a3a824442f662613a8808e893e7b7 MISC metadata.xml 347 BLAKE2B f003b9e0541ffd38d84b2daf8b4df59bfbec1510ae162ac42af1cb1cb110f19297074d61b9b84d71441a0ceba9acbd38123db467e8500c482165fcd6c7e7b90b SHA512 8610e747bbc86428757f77ed688520cdd9efeabc08e08f99ce74d98e7763f3f8cb7648b1eea01bc4db79ae16a650cb119b82022d1ac41e8fcbd6a6b40385e580 diff --git a/sci-biology/poa/files/poa-2-fno-common.patch b/sci-biology/poa/files/poa-2-fno-common.patch new file mode 100644 index 000000000000..ddd738a5524c --- /dev/null +++ b/sci-biology/poa/files/poa-2-fno-common.patch @@ -0,0 +1,13 @@ +--- a/black_flag.h ++++ b/black_flag.h +@@ -236,8 +236,8 @@ + int sourceline, + char sourcefile_revision[]); + +-char *Program_name; +-char *Program_version; ++extern char *Program_name; ++extern char *Program_version; + + void black_flag_init(char progname[],char progversion[]); + void black_flag_init_args(int narg,char *arg[],char progversion[]); diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch index bdd638cf64b7..fb01f0b5f934 100644 --- a/sci-biology/poa/files/2-respect-flags.patch +++ b/sci-biology/poa/files/poa-2-respect-flags.patch @@ -1,26 +1,38 @@ -diff --git a/Makefile b/Makefile -index a65bed0..713a7ab 100644 --- a/Makefile +++ b/Makefile -@@ -26,9 +26,10 @@ LIBOBJECTS= \ +@@ -1,6 +1,3 @@ +- +-AR=ar rc +- + TARGETS=poa liblpo.a poa_doc libbflag.a + + # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS +@@ -26,9 +23,8 @@ stringptr.o -CC = gcc -+CC ?= gcc #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -+OPT_CFLAGS = -g -+CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. # -I$(HOME)/lib/include # -DREPORT_MAX_ALLOC -@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS) +@@ -37,14 +33,14 @@ + + liblpo.a: $(LIBOBJECTS) + rm -f $@ +- $(AR) $@ $(LIBOBJECTS) +- ranlib $@ ++ $(AR) rc $@ $(LIBOBJECTS) ++ $(RANLIB) $@ + + # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!! poa: $(OBJECTS) liblpo.a - $(CC) -o $@ $(OBJECTS) -lm liblpo.a -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a what: @echo poa: partial-order based sequence alignment program diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild index fc472ce96007..d87f2a638117 100644 --- a/sci-biology/poa/poa-2-r1.ebuild +++ b/sci-biology/poa/poa-2-r1.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_P="${PN}V${PV}" @@ -15,30 +15,30 @@ SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="static-libs" S="${WORKDIR}/${MY_P}" -src_prepare() { - epatch "${FILESDIR}"/${PV}-respect-flags.patch +PATCHES=( + "${FILESDIR}"/${P}-respect-flags.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_configure() { + tc-export AR CC RANLIB } src_compile() { - emake \ - CC="$(tc-getCC)" \ - OPT_CFLAGS="${CFLAGS}" \ - poa + emake poa } src_install() { - dobin "${S}"/poa "${S}"/make_pscores.pl - use static-libs && dolib.a "${S}"/liblpo.a - dodoc "${S}"/README "${S}"/multidom.* + dobin poa make_pscores.pl + dodoc README multidom.* insinto /usr/share/poa - doins "${S}"/*.mat + doins *.mat } pkg_postinst() { elog "poa requires a score matrix as the first argument." - elog "This package installs two examples to ${EROOT}usr/share/poa/." + elog "This package installs two examples to ${EROOT}/usr/share/poa/." } diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest index 93ed6d8adf22..0de0a4ebedfe 100644 --- a/sci-biology/vienna-rna/Manifest +++ b/sci-biology/vienna-rna/Manifest @@ -1,10 +1,6 @@ -AUX vienna-rna-2.1.1-bindir.patch 361 BLAKE2B c05d660b422519274f3c88c922d9eac79a8af055df17b78ecfd13561e76f02820d0bdc0462b66100858a8e6b1f3f8bba41cacbc142b9684e47aeb11295edef93 SHA512 f2e9da29f1ae3c1d3e7594367ef13ad0d44ebbcf1d9badf9d55c415e50b7e5af170dba7bcdad6438505786b941518f84ddb154cf1a6df60a229f3856cf333a94 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-2.1.1-setup.py 810 BLAKE2B 7db99496739eaf21a8964d8a545204c05026ae6e5de1070d14e820e64760ffb2544a2a0247543415cc909d8938ac423be7d57dddd68103e3d9cc007ac7db7833 SHA512 57feac6d5701a25fcda01f93f506a422d4639595a7d0ef73575af88f283fabc3730a8ea3e116ccfd417b015611c813f08ff047c9e362eaa74d2ce275ae65f8b8 AUX vienna-rna-2.1.8-bindir.patch 367 BLAKE2B 9bf3df6c604d5ac0661188d4f662ee12387f8bb30c2e3ecbd4a7bfd0a73ff5419f7a10b2fe70efd53e4b634bfdd3c1039ec000b26e7f5edbbcc4242a4edf5914 SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf -DIST ViennaRNA-2.1.1.tar.gz 5327215 BLAKE2B 1319a13daafc3798b792f43488590b4d1d290cbbf41ed6e401255c082eceb1212c312179ea31c3e574c852b453a1641198768bf565e72a920b433420d259c53f SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e -EBUILD vienna-rna-2.1.1.ebuild 2667 BLAKE2B f81e3a8fd09cc846b570831ee21081e246163cfa36990a42c1e582b47adb8f59b137bd656277ed1b990a0fdddbfbc67e6c49d22a896c78842362bd1e16eaab0d SHA512 22b96fce6750fd8094e6943abd8085ec5e3035f66766f56a6a840f591faaebbffece2b0174e7db078d4e96bae30762bc6d15e21bc2e45a6e086115ddb2ca4bc1 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-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch deleted file mode 100644 index 6d35ecea9b0f..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-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 = $(prefix)/bin - pkgbin_PROGRAMS = b2ct popt - - pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py deleted file mode 100644 index 57f6b712ba3d..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py +++ /dev/null @@ -1,27 +0,0 @@ -from distutils.core import setup, Extension -import os -import sys - -old_filename = os.path.join("Perl", "RNA.py") -new_filename = os.path.join("Perl", "__init__.py") -if os.path.exists(old_filename): - os.rename(old_filename, new_filename) - -extra_link_args = [] - -extension = Extension("_RNA", - ["Perl/RNA_wrap.c"], - libraries=['RNA'], - library_dirs=['lib'], - extra_link_args=extra_link_args - ) - -setup(name="RNA", - version="2.1.1", - description="Vienna RNA", - author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", - url="http://www.tbi.univie.ac.at/RNA/", - package_dir = {'RNA':'Perl'}, - packages = ['RNA'], - ext_modules=[extension], - ) diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild deleted file mode 100644 index 8b760b5a84bf..000000000000 --- a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild +++ /dev/null @@ -1,111 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_OPTIONAL=true -AUTOTOOLS_AUTORECONF=true -AUTOTOOLS_IN_SOURCE_BUILD=1 - -inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs - -DESCRIPTION="RNA secondary structure prediction and comparison" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" -SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${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 - "${FILESDIR}"/${P}-prll.patch - "${FILESDIR}"/${P}-impl-decl.patch -) - -src_prepare() { - sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die - sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die - - autotools-utils_src_prepare - - if use python; then - cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die - 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:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \ - -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \ - -i RNAforester/g2-0.70/Makefile || die - sed \ - -e "s:CC=gcc:CC=$(tc-getCC):" \ - -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ - -i Readseq/Makefile || die - use python && distutils-r1_src_configure -} - -src_compile() { - autotools-utils_src_compile - autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) - - # TODO: Add (optional?) support for the NCBI toolkit. - if use python; then - pushd Perl > /dev/null - mv RNA_wrap.c{,-perl} || die - swig -python RNA.i || die - popd > /dev/null - distutils-r1_src_compile - mv Perl/RNA_wrap.c{-perl,} || die - fi -} - -src_test() { - autotools-utils_src_compile -C Perl 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" - use python && distutils-r1_src_install -} diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest index 1cb622926ec9..e45ac70e7741 100644 --- a/sci-biology/wgs-assembler/Manifest +++ b/sci-biology/wgs-assembler/Manifest @@ -1,5 +1,5 @@ -AUX wgs-assembler-7.0-build.patch 10279 BLAKE2B 9fd4a113d4ea3b07570c39e32892b535a0ed7d0e958602ca891c75fa3aa73a44d205fe43580e43d98cdafa1d431c12f68d5fe55e52aca82e451d5aae3ea2c551 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9 +AUX wgs-assembler-7.0-build.patch 10479 BLAKE2B 906d057017be1b84b65812f5ee28b56a34c5a2a34e03d826270cf819e63363fbb72cef90884ce5df04db2758f662b76bbd46aab79fb53452fecd99a6be179c59 SHA512 524baaeaf66ab74ac4c0649e241c0d3f070b087b89a8b723c8886c280ea9ca8a78bdb83cdc32237965c9faf04faf97edb22587d9fdc6db345f3e8dfbf1a3e9b0 AUX wgs-assembler-7.0-libtirpc.patch 516 BLAKE2B 1ee7876f767e559a008d86b8f6ccdbf70763646b782ea23d2bc9f74edab84ff633270ff15d0cd5b888674c5ee0d0bdcd3b73a48bf040f06f2a56bf4e366125cf SHA512 b2a29b2dc0578d4e8544dce258327a34ac4a5ca6bea3e901bee06d89618e9cba7f569fd54da6148372826d053829bc991db7c4cfd5a8564dd81545566698c947 DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba -EBUILD wgs-assembler-7.0-r2.ebuild 1662 BLAKE2B 1c542685f8667e1901eb3950c084ad386e29a077d280e5c3ed24ae84fed71e4876a5c8bed80ea33c4b7b4c3b0c0720f0229d3efc1e2f1654548cdfeb32383e5b SHA512 ad0f1a44e14c9c714b7b6d00dda05bb9b16b9bdde29989d2fd4d785294053aae94d85d0b5ab92faeb2574e99f18a6c566c2c8cc01c5d920632a480aae6f88a4e +EBUILD wgs-assembler-7.0-r2.ebuild 1492 BLAKE2B cea99ff2f1c8d6d6d2b08e23808480d6b2018d6741a8e18a0a09e90f8792139af499617fe9b70723257ef7b3d63a6f270acbf06d8a426eeda3f8b59485424237 SHA512 3eb63c55dc920cf70e3da4562c7e96cd14bd646f1d7cdf74cb58ee80fdffdbdd0fe6d0a0bce2d3e01450c1fd82ad6db3bee79e46b795e2c98357a314a13bd841 MISC metadata.xml 354 BLAKE2B eaf844f74ea3b2a51cba2f00ebc0a3cc895312e04a995000e93426fa0e2f9d8601edb2011ff6c837f85b3a5755b819dc7ce517d3787c2e7bd37e097e144fb156 SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193 diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch index f7fb44743968..238541b512f2 100644 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch +++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch @@ -1,33 +1,6 @@ - kmer/Make.rules | 4 ++-- - kmer/configure.sh | 20 +++++++++---------- - src/c_make.as | 58 +++++++++++++++++++++++++++---------------------------- - src/c_make.gen | 4 ++-- - 4 files changed, 43 insertions(+), 43 deletions(-) - -diff --git a/kmer/Make.rules b/kmer/Make.rules -index f904b13..5c2d477 100644 ---- a/kmer/Make.rules -+++ b/kmer/Make.rules -@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:% - ## EXE targets - ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) - ${ALL_C_EXES}: -- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} -+ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} - __SUBGOALS__+=$${${1:.=.C_EXES}} - - ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) - ${ALL_CXX_EXES}: -- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} -+ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} - __SUBGOALS__+=$${${1:.=.CXX_EXES}} - - define .RULE-install-copy-C-CXX-EXES -diff --git a/kmer/configure.sh b/kmer/configure.sh -index 2f0d5ea..9daf89f 100755 --- a/kmer/configure.sh +++ b/kmer/configure.sh -@@ -254,13 +254,13 @@ EOF +@@ -254,13 +254,13 @@ # -*- makefile -*- # Linux, optimized CC := $CC @@ -46,7 +19,7 @@ index 2f0d5ea..9daf89f 100755 CXXLIBS := -pthread -ldl ARFLAGS := ruvs INSTALL/ := $target/ -@@ -272,13 +272,13 @@ EOF +@@ -272,13 +272,13 @@ # -*- makefile -*- # Linux64, optimized CC := $CC @@ -65,11 +38,37 @@ index 2f0d5ea..9daf89f 100755 CXXLIBS := -pthread -ldl ARFLAGS := ruvs INSTALL/ := $target/ -diff --git a/src/c_make.as b/src/c_make.as -index 0172807..4304589 100644 +@@ -401,8 +401,8 @@ + .O := .o + CLD := \${CC} + CXXLD := \${CXX} +-CCDEP := gcc -MM -MG +-CXXDEP := g++ -MM -MG ++CCDEP := \$(CC) -MM -MG ++CXXDEP := \$(CXX) -MM -MG + CLIBS += -lm -lbz2 + CXXLIBS += -lm -lbz2 + PYTHON := $PYTHON +--- a/kmer/Make.rules ++++ b/kmer/Make.rules +@@ -139,12 +139,12 @@ + ## EXE targets + ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) + ${ALL_C_EXES}: +- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} ++ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} + __SUBGOALS__+=$${${1:.=.C_EXES}} + + ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) + ${ALL_CXX_EXES}: +- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} ++ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} + __SUBGOALS__+=$${${1:.=.CXX_EXES}} + + define .RULE-install-copy-C-CXX-EXES --- a/src/c_make.as +++ b/src/c_make.as -@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen +@@ -64,27 +64,27 @@ ifeq ($(OSTYPE), Linux) ifeq ($(MACHINETYPE), i686) @@ -107,7 +106,7 @@ index 0172807..4304589 100644 endif endif -@@ -94,19 +94,19 @@ endif +@@ -94,19 +94,19 @@ ifeq ($(OSTYPE), FreeBSD) ifeq ($(MACHINETYPE), i386) @@ -134,7 +133,16 @@ index 0172807..4304589 100644 else ifeq ($(BUILDDEBUG), 1) ARCH_CFLAGS += -g -@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) +@@ -126,8 +126,6 @@ + + + ifeq ($(OSTYPE), Darwin) +- CC = gcc +- CXX = g++ + ARCH_CFLAGS = -D_THREAD_SAFE + + ifeq ($(MACHINETYPE), ppc) +@@ -140,14 +138,14 @@ ifeq ($(MACHINETYPE), i386) ifeq ($(BUILDDEBUG), 1) @@ -153,7 +161,7 @@ index 0172807..4304589 100644 endif endif -@@ -161,23 +161,23 @@ endif +@@ -161,23 +159,23 @@ ifeq ($(OSTYPE), SunOS) ifeq ($(MACHINETYPE), i86pc) ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads @@ -182,7 +190,7 @@ index 0172807..4304589 100644 endif endif -@@ -186,14 +186,14 @@ endif +@@ -186,14 +184,14 @@ ifeq ($(BUILDPROFILE), 1) ARCH_CFLAGS += -pg @@ -199,7 +207,7 @@ index 0172807..4304589 100644 LDFLAGS += $(ARCH_LDFLAGS) INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) -@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) +@@ -205,7 +203,7 @@ OBJ_SEARCH_PATH = $(LOCAL_OBJ) ifeq ($(SITE_NAME), JCVI) @@ -208,11 +216,31 @@ index 0172807..4304589 100644 endif # The order of compilation here is very carefully chosen to be the -diff --git a/src/c_make.gen b/src/c_make.gen -index 7b5227c..c27b777 100644 --- a/src/c_make.gen +++ b/src/c_make.gen -@@ -396,12 +396,12 @@ $(LIBRARIES): +@@ -248,10 +248,6 @@ + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC=gcc +-endif +- + ifneq "$(origin CPPFLAGS)" "environment" + CPPFLAGS= + endif +@@ -264,10 +260,6 @@ + CDEFS= + endif + +-ifneq "$(origin CXX)" "environment" +-CXX=g++ +-endif +- + ifneq "$(origin CXXFLAGS)" "environment" + CXXFLAGS= + endif +@@ -396,12 +388,12 @@ $(C_PROGS): @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; cd $(LOCAL_OBJ); \ diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild index fc5869667f02..a9193dfe1807 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" @@ -12,7 +12,6 @@ SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 x86" -IUSE="static-libs" DEPEND=" net-libs/libtirpc @@ -29,13 +28,10 @@ PATCHES=( "${FILESDIR}"/${P}-libtirpc.patch ) -src_prepare() { - default - tc-export CC CXX -} - src_configure() { - cd "${S}/kmer" + tc-export AR CC CXX + + cd kmer || die ./configure.sh || die } @@ -57,16 +53,14 @@ src_install() { sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die dobin kmer/${MY_S}/bin/* - insinto /usr/$(get_libdir)/${PN} - use static-libs && doins kmer/${MY_S}/lib/* insinto /usr/include/${PN} - doins kmer/${MY_S}/include/* + doins -r kmer/${MY_S}/include/. insinto /usr/share/${PN}/lib doins -r ${MY_S}/bin/TIGR rm -rf ${MY_S}/bin/TIGR || die dobin ${MY_S}/bin/* - use static-libs && dolib.a ${MY_S}/lib/* + dodoc README } |