diff options
| author | Alexey Dokuchaev <danfe@FreeBSD.org> | 2013-02-25 13:00:15 +0000 |
|---|---|---|
| committer | Alexey Dokuchaev <danfe@FreeBSD.org> | 2013-02-25 13:00:15 +0000 |
| commit | bb8c521c7258520930e8fe66783165fa34cc90f9 (patch) | |
| tree | bb5cfa6c6a4d2d0dd087d1f53e80daaf635bed51 /biology | |
| parent | 77ffd594140b1d9a25012f6e1b3f9c75b8a9b214 (diff) | |
| download | ports-bb8c521c7258520930e8fe66783165fa34cc90f9.tar.gz ports-bb8c521c7258520930e8fe66783165fa34cc90f9.zip | |
Notes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/ugene/Makefile | 3 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp | 2 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp | 30 | ||||
| -rw-r--r-- | biology/ugene/pkg-plist | 3 |
4 files changed, 37 insertions, 1 deletions
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 9828a43a2a47..6897e859952d 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -31,6 +31,9 @@ MANCOMPRESSED= yes .if ${ARCH} == "amd64" # need to manually tell the build we are on x64 CARCH= CONFIG+=x64 +PLIST_SUB= NOX64="@comment " +.else +PLIST_SUB= NOX64="" .endif # yes, bash is required, stuff will not execute with sh diff --git a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp index 42a782ad317b..1e5e161bac43 100644 --- a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp +++ b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp @@ -1,4 +1,4 @@ ---- ./src/corelibs/U2Private/src/CrashHandler.cpp.old 2012-10-30 15:36:22.000000000 +0100 +--- ./src/corelibs/U2Private/src/CrashHandler.cpp.orig 2012-10-30 15:36:22.000000000 +0100 +++ ./src/corelibs/U2Private/src/CrashHandler.cpp 2012-10-30 15:47:47.000000000 +0100 @@ -253,7 +253,7 @@ } diff --git a/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp b/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp new file mode 100644 index 000000000000..f9f6d167af29 --- /dev/null +++ b/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp @@ -0,0 +1,30 @@ +--- ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp.orig 2012-12-26 17:43:44.000000000 +0800 ++++ ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp 2013-02-25 17:25:06.000000000 +0800 +@@ -9,13 +9,6 @@ + return (PROB) pow(2.0, (double) Score/INTSCALE); + } + +-static const double log2e = log2(exp(1.0)); +- +-double lnTolog2(double ln) +- { +- return ln*log2e; +- } +- + double log2(double x) + { + if (0 == x) +@@ -27,6 +20,13 @@ + return log(x)*dInvLn2; + } + ++static const double log2e = log2(exp(1.0)); ++ ++double lnTolog2(double ln) ++ { ++ return ln*log2e; ++ } ++ + SCORE ProbToScore(PROB Prob) + { + if (0.0 == Prob) diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 86d67cf6f169..927adce7aa40 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -88,6 +88,7 @@ lib/ugene/plugins/librepeat_finder.so lib/ugene/plugins/libsitecon.so lib/ugene/plugins/libsmith_waterman.so lib/ugene/plugins/libtest_runner.so +%%NOX64%%lib/ugene/plugins/libumuscle.so lib/ugene/plugins/libweight_matrix.so lib/ugene/plugins/libworkflow_designer.so lib/ugene/plugins/opencl_support.license @@ -118,6 +119,8 @@ lib/ugene/plugins/smith_waterman.license lib/ugene/plugins/smith_waterman.plugin lib/ugene/plugins/test_runner.license lib/ugene/plugins/test_runner.plugin +%%NOX64%%lib/ugene/plugins/umuscle.license +%%NOX64%%lib/ugene/plugins/umuscle.plugin lib/ugene/plugins/weight_matrix.license lib/ugene/plugins/weight_matrix.plugin lib/ugene/plugins/workflow_designer.license |