<pre style='margin:0'>
Kurt Hindenburg (kurthindenburg) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/f190e1b8b3a1279049f21957e60831371939be47">https://github.com/macports/macports-ports/commit/f190e1b8b3a1279049f21957e60831371939be47</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new f190e1b samtools: update to 1.3.1
</span>f190e1b is described below
<span style='display:block; white-space:pre;color:#808000;'>commit f190e1b8b3a1279049f21957e60831371939be47
</span>Author: Kurt Hindenburg <khindenburg@macports.org>
AuthorDate: Sat Mar 4 17:45:37 2017 -0500
<span style='display:block; white-space:pre;color:#404040;'> samtools: update to 1.3.1
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> enable tests which require 2 patches; change eval usage
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> closes https://trac.macports.org/ticket/50202
</span>---
science/samtools/Portfile | 16 +++++++++++-----
science/samtools/files/patch-Makefile-test.diff | 13 +++++++++++++
.../files/patch-fix-test-cant-open-terminal.diff | 21 +++++++++++++++++++++
3 files changed, 45 insertions(+), 5 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 3fd1b78..4606a52 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;'>@@ -3,8 +3,7 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup samtools samtools 1.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup samtools samtools 1.3.1
</span> categories science
platforms darwin
maintainers gmail.com:haroldpimentel openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -17,13 +16,16 @@ 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 536dcdc1c7730bc4a93f68e39967890331211c24 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 aecfeaff2aaf23fb2de59421eb48eafe3be6df77 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e
</span>
homepage http://www.htslib.org/
github.tarball_from releases
use_bzip2 yes
<span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-fix-test-cant-open-terminal.diff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-Makefile-test.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> depends_lib port:zlib port:ncurses
use_configure no
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -37,10 +39,14 @@ destroot {
</span> xinstall -m 644 ${worksrcpath}/libbam.a ${destroot}${prefix}/lib
xinstall -m 644 ${worksrcpath}/samtools.1 ${destroot}${prefix}/share/man/man1
xinstall -d ${destroot}${prefix}/include/bam
<span style='display:block; white-space:pre;background:#ffe0e0;'>- eval xinstall -m 644 [glob ${worksrcpath}/*.h] ${destroot}${prefix}/include/bam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 644 {*}[glob ${worksrcpath}/*.h] ${destroot}${prefix}/include/bam
</span>
xinstall -d ${destroot}${prefix}/share/doc/${name}
xinstall -m 644 -W ${worksrcpath} \
AUTHORS LICENSE NEWS README \
${destroot}${prefix}/share/doc/${name}
}
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+test.run yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+test.target check
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_test-append port:htslib
</span><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>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..2019244
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/samtools/files/patch-Makefile-test.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,13 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile 2016-04-22 05:51:16.000000000 -0400
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2017-03-04 17:36:30.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -197,8 +197,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # For tests that might use it, set $REF_PATH explicitly to use only reference
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # areas within the test suite (or set it to ':' to use no reference areas).
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # (regression.sh sets $REF_PATH to a subdirectory itself.)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++check test: samtools $(BUILT_TEST_PROGRAMS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ REF_PATH=: test/test.pl
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ test/merge/test_bam_translate test/merge/test_bam_translate.tmp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ test/merge/test_rtrans_build
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 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>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..7a882aa
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/samtools/files/patch-fix-test-cant-open-terminal.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,21 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://github.com/samtools/samtools/commit/ce4a601a0859bc9ccfcf000dddf0ac77e7d576b3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+diff --git a/test/test.pl b/test/test.pl
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+index 5042541..c0a3380 100755
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- test/test.pl
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ test/test.pl
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -547,13 +547,12 @@ sub test_usage
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if (-t) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ $args{redirection} = ""; # no redirection necessary
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- elsif (eval { require IO::Pty }) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- $tty_input = new IO::Pty;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ elsif (eval { require IO::Pty; $tty_input = new IO::Pty; }) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # ensure stdin is a terminal, so that subcommands display their usage
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ $args{redirection} = "<'" . $tty_input->ttyname . "'";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- warn "$0: module IO::Pty not found; skipping usage tests\n";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ warn "$0: no IO::Pty module or can't open pty; skipping usage tests\n";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ return;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span></pre><pre style='margin:0'>
</pre>