<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/e72cbc2b73c19839cc1a29d521ce5d61e45cb326">https://github.com/macports/macports-ports/commit/e72cbc2b73c19839cc1a29d521ce5d61e45cb326</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 e72cbc2  cufflinks: Update to 2.2.1
</span>e72cbc2 is described below

<span style='display:block; white-space:pre;color:#808000;'>commit e72cbc2b73c19839cc1a29d521ce5d61e45cb326
</span>Author: Ryan Schmidt <ryandesign@macports.org>
AuthorDate: Tue Oct 23 02:25:36 2018 -0500

<span style='display:block; white-space:pre;color:#404040;'>    cufflinks: Update to 2.2.1
</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/42120
</span>---
 science/cufflinks/Portfile          | 57 ++++++++++++++++++++++++++-----------
 science/cufflinks/files/boost.patch | 12 ++++++++
 2 files changed, 52 insertions(+), 17 deletions(-)

<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/cufflinks/Portfile b/science/cufflinks/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index d2b0750..3d61d0a 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/cufflinks/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/cufflinks/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,12 +1,17 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> PortSystem          1.0
<span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup           github 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup        cole-trapnell-lab cufflinks 2.2.1 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  6378571ecb06971d1dff5b6ef81a55b36a8be498\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    766280
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-name                cufflinks
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             0.9.3
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            2
</span> categories          science biology
 platforms           darwin
<span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers         nomaintainer
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-license             Boost
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers         {ryandesign @ryandesign} openmaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license             Boost-1
</span> 
 description         Cufflinks assembles transcripts, estimates their abundances,\
                     and tests for differential expression and regulation in RNA-Seq samples.
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -18,24 +23,42 @@ long_description    Cufflinks assembles transcripts, estimates their abundances,
</span>                     Cufflinks then estimates the relative abundances of these \
                     transcripts based on how many reads support each one.
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            http://cufflinks.cbcb.umd.edu/
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites        ${homepage}downloads
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage            http://${github.author}.github.io/${github.project}/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites        ${homepage}assets/downloads/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build       port:samtools
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib         port:boost \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:eigen3 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:htslib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:zlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles          boost.patch
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args      --with-bam=${prefix} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    --with-boost=${prefix} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    --with-eigen=${prefix} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    --with-zlib=${prefix}
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           sha1        f6c28d8f98569f8d1eae72ff050ce7d2d06bfba4\
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    rmd160      b9b3b8ec322e79e0e6f2b4b2f23de27b58ec44f4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://github.com/cole-trapnell-lab/cufflinks/issues/17
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://github.com/cole-trapnell-lab/cufflinks/issues/100
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.cppflags-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    -isystem${prefix}/include/eigen3
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib         port:zlib \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:samtools \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:boost
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.ldflags-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    -lboost_serialization-mt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    -lboost_thread-mt
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# samtools is not universal
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-universal_variant   no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://github.com/cole-trapnell-lab/cufflinks/issues/62
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.ldflags-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    -lhts
</span> 
 post-destroot {
<span style='display:block; white-space:pre;background:#ffe0e0;'>-    xinstall -d ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-    xinstall -m 644 -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    set docdir ${prefix}/share/doc/${subport}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    xinstall -d ${destroot}${docdir}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    xinstall -m 0644 -W ${worksrcpath} \
</span>         AUTHORS \
         LICENSE \
         README \
<span style='display:block; white-space:pre;background:#ffe0e0;'>-        ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+        ${destroot}${docdir}
</span> }
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/cufflinks/files/boost.patch b/science/cufflinks/files/boost.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..f78641c
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/cufflinks/files/boost.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Remove references to tr1 which was removed from boost in version 1.65.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/biascorrection.h.orig      2014-03-24 16:54:47.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/biascorrection.h   2018-10-23 01:37:26.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -15,7 +15,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <vector>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <list>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <string>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#include <boost/tr1/unordered_map.hpp>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#include <boost/unordered_map.hpp>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <boost/thread.hpp>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include "common.h"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
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</pre>