<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/3e5b4f8e3b96e989f67c687bef48d97a6af44b6f">https://github.com/macports/macports-ports/commit/3e5b4f8e3b96e989f67c687bef48d97a6af44b6f</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 3e5b4f8 bedtools: update to v2.29.2
</span>3e5b4f8 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 3e5b4f8e3b96e989f67c687bef48d97a6af44b6f
</span>Author: Arjan van der Velde <vandervelde.ag@gmail.com>
AuthorDate: Tue Mar 17 16:34:44 2020 -0400
<span style='display:block; white-space:pre;color:#404040;'> bedtools: update to v2.29.2
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> This updates bedtools from v2.28.0 to v2.29.2 and also changes its
</span><span style='display:block; white-space:pre;color:#404040;'> dependence on py27-sphinx to py38-sphinx in order to prevent pulling
</span><span style='display:block; white-space:pre;color:#404040;'> in python2. Changes also reflect the updated bedtools license.
</span>---
science/bedtools/Portfile | 28 ++++++++++------------
...rc-utils-BamTools-include-BamAlignment.hpp.diff | 12 ----------
...h-src-utils-BamTools-include-SamHeader.hpp.diff | 12 ----------
3 files changed, 12 insertions(+), 40 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/Portfile b/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 9e6bf6f..bc0643c 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -2,15 +2,14 @@
</span>
PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup cxx11 1.1
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup arq5x bedtools2 2.28.0 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup arq5x bedtools2 2.29.2 v
</span>
name bedtools
categories science
platforms darwin
maintainers {gmail.com:vandervelde.ag @arjanvandervelde} openmaintainer
<span style='display:block; white-space:pre;background:#ffe0e0;'>-license GPL-2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license MIT
</span>
description Utilities to perform basic operations on BED files
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -19,13 +18,15 @@ long_description The BEDTools utilities allow one to address common genomics
</span> The utilities are largely based on four widely-used file formats: \
BED, GFF/GTF, VCF, and SAM/BAM.
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 0807fc84acd6d80f646ee387943ff6345203396a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 511d8623038836ac8d1f9e260016867494b9040de65d0f0f1eb7feac7b698bbd \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 20565042
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 25eefac3397b98c1c055de92c9cbb360ee4efb59 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 66d4d74000549fd5a1f939dc2bc0417d743dec72575a709213058754ff6dd146 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 20638903
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_build port:py27-sphinx
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+compiler.cxx_standard 2011
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib-append port:zlib port:xz
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build port:py38-sphinx
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib port:xz port:bzip2
</span>
use_configure no
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -34,21 +35,16 @@ build.args-append CC=${configure.cc} \
</span>
use_parallel_build yes
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-src-utils-BamTools-include-BamAlignment.hpp.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> post-build {
<span style='display:block; white-space:pre;background:#ffe0e0;'>- system -W ${worksrcpath}/docs "${build.cmd} SPHINXBUILD=${prefix}/bin/sphinx-build-2.7 html man"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ system -W ${worksrcpath}/docs "${build.cmd} SPHINXBUILD=${prefix}/bin/sphinx-build-3.8 html man"
</span> }
destroot {
xinstall -m 755 {*}[glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin/
xinstall -d ${destroot}${prefix}/share/doc/${name}
xinstall -d ${destroot}${prefix}/share/${name}/genomes
<span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -m 644 -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- LICENSE README.md RELEASE_HISTORY \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -m 644 {*}[glob ${worksrcpath}/genomes/*] ${destroot}${prefix}/share/${name}/genomes/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 644 -W ${worksrcpath} LICENSE README.md ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 644 {*}[glob ${worksrcpath}/genomes/*] ${destroot}${prefix}/share/${name}/genomes/
</span> copy ${worksrcpath}/docs/_build/html ${destroot}${prefix}/share/doc/${name}/html
xinstall -m 644 ${worksrcpath}/docs/_build/man/bedtools.1 ${destroot}${prefix}/share/man/man1
}
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff b/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 4190f37..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,12 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git src/utils/BamTools/include/BamAlignment.hpp src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index f7da717d..db01a2f4 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -3,6 +3,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <stdint.h>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <memory>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <cstring>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include <stdlib.h>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- namespace BamTools {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const static char cigar_ops_as_chars[] = { 'M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', 'B' };
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static inline std::string _mkstr(const uint8_t* what) { return std::string((const char*)what + 1); }
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff b/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index cd2dacf..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,12 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git src/utils/BamTools/include/SamHeader.hpp src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 1024370e..06d22be6 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6,6 +6,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <vector>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <string.h>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <api/BamAux.h>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include <stdlib.h>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- namespace BamTools {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- typedef std::vector<RefData> RefVector;
</span></pre><pre style='margin:0'>
</pre>