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| author | Piotr Kubaj <pkubaj@FreeBSD.org> | 2019-06-21 11:43:09 +0000 |
|---|---|---|
| committer | Piotr Kubaj <pkubaj@FreeBSD.org> | 2019-06-21 11:43:09 +0000 |
| commit | ba101b3372ded51df2ef5672b2b48918873fa42e (patch) | |
| tree | 8ab4aa9eac6b4179fcf4d94ae9c6bb643702d0f8 /biology/abyss | |
| parent | 5bbda70d09c66ab393a3e9e954761fb19cc0716e (diff) | |
| download | ports-ba101b3372ded51df2ef5672b2b48918873fa42e.tar.gz ports-ba101b3372ded51df2ef5672b2b48918873fa42e.zip | |
biology/abyss: fix build on big-endian architectures
Use new GCC from ports on GCC architectures.
Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures.
Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ).
PR: 238737
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20717
Notes
Notes:
svn path=/head/; revision=504788
Diffstat (limited to 'biology/abyss')
| -rw-r--r-- | biology/abyss/Makefile | 5 | ||||
| -rw-r--r-- | biology/abyss/distinfo | 4 | ||||
| -rw-r--r-- | biology/abyss/files/patch-Common_city.cc | 13 |
3 files changed, 20 insertions, 2 deletions
diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index 482193836c85..d1eb83c9b86f 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -6,6 +6,9 @@ PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ +PATCH_SITES= https://github.com/bcgsc/${PORTNAME}/commit/ +PATCHFILES= 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1 + MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler @@ -21,7 +24,7 @@ LIB_DEPENDS= libffi.so:devel/libffi \ RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake -USES= gmake iconv:wchar_t localbase:ldflags shebangfix sqlite +USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite SHEBANG_FILES= bin/${PORTNAME}-* SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo index 1e1588ec91ed..41338e6eb31f 100644 --- a/biology/abyss/distinfo +++ b/biology/abyss/distinfo @@ -1,3 +1,5 @@ -TIMESTAMP = 1551061546 +TIMESTAMP = 1561103807 SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 SIZE (abyss-2.1.5.tar.gz) = 1201318 +SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934 +SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701 diff --git a/biology/abyss/files/patch-Common_city.cc b/biology/abyss/files/patch-Common_city.cc new file mode 100644 index 000000000000..9fc7031b6639 --- /dev/null +++ b/biology/abyss/files/patch-Common_city.cc @@ -0,0 +1,13 @@ +--- Common/city.cc.orig 2018-09-21 23:44:14 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) + ++#elif defined(__FreeBSD__) ++#include <sys/endian.h> ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) + #else + #include <byteswap.h> + #endif |