<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/e6904a6282252b88211c829bb7153c251b4c33f4">https://github.com/macports/macports-ports/commit/e6904a6282252b88211c829bb7153c251b4c33f4</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit e6904a6282252b88211c829bb7153c251b4c33f4
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Thu Jan 17 06:00:34 2019 -0700
<span style='display:block; white-space:pre;color:#404040;'> bowtie2: update version 2.2.9->2.3.4.3
</span>---
science/bowtie2/Portfile | 30 +++++++------------
science/bowtie2/files/patch-src-Makefile.diff | 43 +++++++++++++--------------
2 files changed, 32 insertions(+), 41 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie2/Portfile b/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 03e0695..17b908e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,8 +3,8 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup BenLangmead bowtie2 2.2.9 v
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BenLangmead bowtie2 2.3.4.3 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span>
categories science biology
platforms darwin
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -26,17 +26,19 @@ long_description Bowtie 2 is an ultrafast and memory-efficient tool \
</span>
homepage http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 4d385888f4cc1dc465cdd74b2e735ca2baed90e8 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 435c27c33807be6227b5370f53146a3e7f890534db650d3d0f5e86570f9d5170 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 5815668
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 ee47b07eaacdb1319ec83c9f01ff46a7c9900933 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 56cf132e1607cb16397c294f0ba1a288aba4eddc1dc10f7ce3e92796f9b1fbc5 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 10574624
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-src-Makefile.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-aligner_result.cpp.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-src-Makefile.diff
</span>
supported_archs x86_64
universal_variant no
installs_libs no
<span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:tbb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> configure.cmd printenv
configure.pre_args
configure.universal_args
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -45,19 +47,9 @@ configure.post_args {>> Makefile.macports.inc}
</span> # replicate values from Makefile prior to patching
configure.optflags -O3 -funroll-loops -g3
<span style='display:block; white-space:pre;background:#ffe0e0;'>-destroot {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -m 755 -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-align-s \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-align-l \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-build \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-build-s \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-build-l \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-inspect \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-inspect-s \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-inspect-l \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ${destroot}${prefix}/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+destroot.args-append prefix=${prefix}
</span>
<span style='display:block; white-space:pre;background:#e0ffe0;'>+post-destroot {
</span> xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name}
xinstall -m 644 -W ${worksrcpath} \
VERSION \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie2/files/patch-src-Makefile.diff b/science/bowtie2/files/patch-src-Makefile.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index 7bf0ce9..e6bc250 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie2/files/patch-src-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie2/files/patch-src-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,6 +1,5 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Respect MacPort compiler flags.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- Makefile.orig 2016-04-21 13:26:11.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2019-01-16 08:31:24.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile.orig 2018-09-16 21:22:55.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2019-01-17 05:35:04.000000000 -0700
</span> @@ -21,6 +21,9 @@
# Makefile for bowtie, bowtie2-build, bowtie2-inspect
#
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -8,30 +7,30 @@ Respect MacPort compiler flags.
</span> +include Makefile.macports.inc
+EXTRA_FLAGS += $(CXXFLAGS)
+
<span style='display:block; white-space:pre;background:#ffe0e0;'>- prefix = /usr/local
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bindir = $(prefix)/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ prefix := /usr/local
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bindir := $(prefix)/bin
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -48,11 +51,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- MACOS = 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -55,12 +58,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MACOS :=
</span> ifneq (,$(findstring Darwin,$(shell uname)))
<span style='display:block; white-space:pre;background:#ffe0e0;'>- MACOS = 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ifneq (,$(findstring 13,$(shell uname -r)))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- CPP = clang++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- CC = clang
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- override EXTRA_FLAGS += -stdlib=libstdc++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MACOS := 1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifeq (1,$(shell uname -r | awk -F. '{ if ($$1 > 12 && $$1 < 16) print 1; }'))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- CXXFLAGS += -stdlib=libstdc++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifdef STATIC_BUILD
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- CXXFLAGS += -mmacosx-version-min=10.9
</span> - endif
endif
POPCNT_CAPABILITY ?= 1
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -167,9 +165,9 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -186,8 +183,8 @@
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>- SSE_FLAG=-msse2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SSE_FLAG := -msse2
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>--DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+DEBUG_FLAGS = $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+RELEASE_FLAGS = $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- NOASSERT_FLAGS = -DNDEBUG
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-DEBUG_FLAGS := -O0 -g3 -m64 $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-RELEASE_FLAGS := -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++DEBUG_FLAGS := $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++RELEASE_FLAGS := $(SSE_FLAG)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ NOASSERT_FLAGS := -DNDEBUG
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ FILE_FLAGS := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
</span></pre><pre style='margin:0'>
</pre>