diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index d023c7d5b8b6..8458e069649a 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -1,51 +1,51 @@ PORTNAME= abyss -DISTVERSION= 2.3.5 -PORTREVISION= 2 +DISTVERSION= 2.3.7 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler WWW= https://www.bcgsc.ca/resources/software/abyss LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= result of comparison of constant 18446744073709551615 with expression of type 'size_t', see https://github.com/bcgsc/abyss/issues/310 BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \ ghc:lang/ghc \ pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer -LIB_DEPENDS= libffi.so:devel/libffi \ +LIB_DEPENDS= libbtllib.so:biology/btllib \ + libffi.so:devel/libffi \ libgmp.so:math/gmp \ libmpich.so:net/mpich # binaries aren't linked with libmpich.so for some reason RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite USE_GITHUB= yes GH_ACCOUNT= bcgsc SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make make_CMD= ${PREFIX}/bin/gmake GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs TEST_TARGET= check # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453 OPTIONS_DEFINE= DOCS PORTDOCS= * PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags .include .if ${OPSYS} == FreeBSD && ( ${OSVERSION} >= 1400079 || ( ${OSVERSION} >= 1302505 && ${OSVERSION} < 1400000 )) CFLAGS+= -Wno-error=unused-but-set-variable .endif .include diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo index 82cc32c0fa85..f27d6fc7904a 100644 --- a/biology/abyss/distinfo +++ b/biology/abyss/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1659120367 -SHA256 (bcgsc-abyss-2.3.5_GH0.tar.gz) = 28fb7d75faa2599c3c4d2d2c29d320612ca1539f1772728d1acdfffb4b82dee5 -SIZE (bcgsc-abyss-2.3.5_GH0.tar.gz) = 3511232 +TIMESTAMP = 1689963359 +SHA256 (bcgsc-abyss-2.3.7_GH0.tar.gz) = eb1d814621ad2accaf19ea009453af891b29663de9f96c0da32c83fbfb71b85e +SIZE (bcgsc-abyss-2.3.7_GH0.tar.gz) = 1323221 diff --git a/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp b/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp deleted file mode 100644 index 01427a36b2ac..000000000000 --- a/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp +++ /dev/null @@ -1,11 +0,0 @@ ---- RResolver/btllib/include/btllib/status.hpp.orig 2022-07-29 18:56:25 UTC -+++ RResolver/btllib/include/btllib/status.hpp -@@ -151,7 +151,7 @@ get_strerror() - char buf[buflen]; - // POSIX and GNU implementation of strerror_r differ, even in function signature - // and so we need to check which one is used --#if __APPLE__ || \ -+#if __APPLE__ || defined(__FreeBSD__) || \ - ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && !_GNU_SOURCE) - strerror_r(errno, buf, buflen); - return buf;