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Fri, 29 Jul 2022 19:57:44 GMT (envelope-from git) Date: Fri, 29 Jul 2022 19:57:44 GMT Message-Id: <202207291957.26TJviLj021920@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 0a752832a5d6 - main - biology/abyss: Update 2.3.1 -> 2.3.5 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7 commit 0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7 Author: Yuri Victorovich AuthorDate: 2022-07-29 19:37:17 +0000 Commit: Yuri Victorovich CommitDate: 2022-07-29 19:57:36 +0000 biology/abyss: Update 2.3.1 -> 2.3.5 --- biology/abyss/Makefile | 6 +++--- biology/abyss/distinfo | 6 +++--- biology/abyss/files/patch-Common_city.cc | 8 ++++---- .../files/patch-RResolver_btllib_include_btllib_status.hpp | 11 +++++++++++ biology/abyss/pkg-plist | 4 +--- 5 files changed, 22 insertions(+), 13 deletions(-) diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index fcfdebd8cc9b..6faf6c0094de 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -1,6 +1,5 @@ PORTNAME= abyss -DISTVERSION= 2.3.1 -PORTREVISION= 1 +DISTVERSION= 2.3.5 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org @@ -15,7 +14,8 @@ 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 \ - libgmp.so:math/gmp + 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 diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo index 864687f7f740..82cc32c0fa85 100644 --- a/biology/abyss/distinfo +++ b/biology/abyss/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1619108885 -SHA256 (bcgsc-abyss-2.3.1_GH0.tar.gz) = b1941d6d975b38d34f41c38b8f4f599fc69d1f37ef3afb71f50318062fb548ea -SIZE (bcgsc-abyss-2.3.1_GH0.tar.gz) = 1531044 +TIMESTAMP = 1659120367 +SHA256 (bcgsc-abyss-2.3.5_GH0.tar.gz) = 28fb7d75faa2599c3c4d2d2c29d320612ca1539f1772728d1acdfffb4b82dee5 +SIZE (bcgsc-abyss-2.3.5_GH0.tar.gz) = 3511232 diff --git a/biology/abyss/files/patch-Common_city.cc b/biology/abyss/files/patch-Common_city.cc index 9fc7031b6639..075c215d82d6 100644 --- a/biology/abyss/files/patch-Common_city.cc +++ b/biology/abyss/files/patch-Common_city.cc @@ -1,8 +1,8 @@ ---- Common/city.cc.orig 2018-09-21 23:44:14 UTC +--- Common/city.cc.orig 2022-05-11 22:23:32 UTC +++ Common/city.cc -@@ -65,6 +65,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) { - #define bswap_32(x) OSSwapInt32(x) - #define bswap_64(x) OSSwapInt64(x) +@@ -70,6 +70,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) { + #define bswap_32(x) bswap32(x) + #define bswap_64(x) bswap64(x) +#elif defined(__FreeBSD__) +#include diff --git a/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp b/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp new file mode 100644 index 000000000000..01427a36b2ac --- /dev/null +++ b/biology/abyss/files/patch-RResolver_btllib_include_btllib_status.hpp @@ -0,0 +1,11 @@ +--- 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; diff --git a/biology/abyss/pkg-plist b/biology/abyss/pkg-plist index 3e2d8eba7135..e40d6907f31b 100644 --- a/biology/abyss/pkg-plist +++ b/biology/abyss/pkg-plist @@ -43,6 +43,7 @@ bin/abyss-map-ssq bin/abyss-mergepairs bin/abyss-overlap bin/abyss-paired-dbg +bin/abyss-paired-dbg-mpi bin/abyss-pe bin/abyss-rresolver-short bin/abyss-samtoafg @@ -54,7 +55,4 @@ bin/abyss-todot bin/abyss-tofastq bin/konnector bin/logcounter -man/man1/ABYSS.1.gz -man/man1/abyss-pe.1.gz man/man1/abyss-sealer.1.gz -man/man1/abyss-tofastq.1.gz