git: 0a752832a5d6 - main - biology/abyss: Update 2.3.1 -> 2.3.5
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Date: Fri, 29 Jul 2022 19:57:44 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7
commit 0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-07-29 19:37:17 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
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 <sys/endian.h>
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