From 90c88731bd036e5698b281fbc0a5f3aa4c9983ac Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 29 Jun 2020 11:38:31 +0100 Subject: gentoo resync : 29.06.2020 --- sci-biology/mcl/Manifest | 5 +- .../mcl/files/mcl-14.137-fix-autotools.patch | 52 +++++++++++++++++++++ .../mcl/files/mcl-14.137-fix-declarations.patch | 53 ++++++++++++++++++++++ .../mcl-14.137-qa-implicit-declarations.patch | 27 ----------- sci-biology/mcl/mcl-14.137.ebuild | 16 +++---- 5 files changed, 115 insertions(+), 38 deletions(-) create mode 100644 sci-biology/mcl/files/mcl-14.137-fix-autotools.patch create mode 100644 sci-biology/mcl/files/mcl-14.137-fix-declarations.patch delete mode 100644 sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch (limited to 'sci-biology/mcl') 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 + 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 + 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-fix-declarations.patch b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch new file mode 100644 index 000000000000..4974d352bf7b --- /dev/null +++ b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch @@ -0,0 +1,53 @@ +Fix QA issues related to implicit declarations. + +* QA Notice: Package triggers severe warnings which indicate that it +* may exhibit random runtime failures. +* 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] + +--- 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" + ++#include "util/alloc.h" + #include "util/io.h" + #include "util/types.h" + #include "util/err.h" +--- a/src/shmcx/mcxi.c ++++ b/src/shmcx/mcxi.c +@@ -8,6 +8,7 @@ + */ + + #include ++#include + + #include "stack.h" + #include "glob.h" diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch deleted file mode 100644 index df4309874d48..000000000000 --- a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch +++ /dev/null @@ -1,27 +0,0 @@ -Fix QA issues related to implicit declarations. - -* QA Notice: Package triggers severe warnings which indicate that it -* may exhibit random runtime failures. -* 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 -@@ -14,6 +14,7 @@ - #include "report.h" - #include "clmadjust.h" - -+#include "util/alloc.h" - #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 -@@ -8,6 +8,7 @@ - */ - - #include -+#include - - #include "stack.h" - #include "glob.h" 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 } -- cgit v1.2.3