<pre style='margin:0'>
Ryan Schmidt (ryandesign) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/4976854457dd7bab71c8612bcf38cac2f0f5fd37">https://github.com/macports/macports-ports/commit/4976854457dd7bab71c8612bcf38cac2f0f5fd37</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 4976854457dd7bab71c8612bcf38cac2f0f5fd37
</span>Author: Ryan Schmidt <ryandesign@macports.org>
AuthorDate: Wed Mar 29 21:49:17 2017 -0500
<span style='display:block; white-space:pre;color:#404040;'> samtools: Update to 1.4
</span>---
science/samtools/Portfile | 11 +++++------
science/samtools/files/patch-Makefile-test.diff | 13 -------------
.../files/patch-fix-test-cant-open-terminal.diff | 21 ---------------------
3 files changed, 5 insertions(+), 40 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/samtools/Portfile b/science/samtools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 4606a52..631c606 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/samtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/samtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,7 +3,7 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup samtools samtools 1.3.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup samtools samtools 1.4
</span> categories science
platforms darwin
maintainers gmail.com:haroldpimentel openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -16,16 +16,13 @@ long_description SAM (Sequence Alignment/Map) Tools provide various \
</span> format, including sorting, merging, indexing and \
generating alignments in a per-position format.
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 aecfeaff2aaf23fb2de59421eb48eafe3be6df77 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 3440638a5b5c9545871672a2659bf90b14e6acf9 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4
</span>
homepage http://www.htslib.org/
github.tarball_from releases
use_bzip2 yes
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-fix-test-cant-open-terminal.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-Makefile-test.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> depends_lib port:zlib port:ncurses
use_configure no
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -49,4 +46,6 @@ destroot {
</span>
test.run yes
test.target check
<span style='display:block; white-space:pre;background:#e0ffe0;'>+test.args {*}${build.args}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> depends_test-append port:htslib
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/samtools/files/patch-Makefile-test.diff b/science/samtools/files/patch-Makefile-test.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 2019244..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/samtools/files/patch-Makefile-test.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,13 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- Makefile 2016-04-22 05:51:16.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2017-03-04 17:36:30.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -197,8 +197,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # For tests that might use it, set $REF_PATH explicitly to use only reference
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # areas within the test suite (or set it to ':' to use no reference areas).
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # (regression.sh sets $REF_PATH to a subdirectory itself.)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+check test: samtools $(BUILT_TEST_PROGRAMS)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ REF_PATH=: test/test.pl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- test/merge/test_bam_translate test/merge/test_bam_translate.tmp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- test/merge/test_rtrans_build
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- test/merge/test_trans_tbl_init
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/samtools/files/patch-fix-test-cant-open-terminal.diff b/science/samtools/files/patch-fix-test-cant-open-terminal.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 7a882aa..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/samtools/files/patch-fix-test-cant-open-terminal.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,21 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# https://github.com/samtools/samtools/commit/ce4a601a0859bc9ccfcf000dddf0ac77e7d576b3
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git a/test/test.pl b/test/test.pl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 5042541..c0a3380 100755
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- test/test.pl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ test/test.pl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -547,13 +547,12 @@ sub test_usage
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (-t) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $args{redirection} = ""; # no redirection necessary
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- elsif (eval { require IO::Pty }) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- $tty_input = new IO::Pty;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ elsif (eval { require IO::Pty; $tty_input = new IO::Pty; }) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # ensure stdin is a terminal, so that subcommands display their usage
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $args{redirection} = "<'" . $tty_input->ttyname . "'";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- warn "$0: module IO::Pty not found; skipping usage tests\n";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ warn "$0: no IO::Pty module or can't open pty; skipping usage tests\n";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span></pre><pre style='margin:0'>
</pre>