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academic/ugene: Update DEP and patched for GCC. 

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Willy Sudiarto Raharjo 2016-06-24 01:36:16 +07:00
parent 3b6994784b
commit f183cad2ff
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GPG Key ID: 887B8374D7333381
3 changed files with 67 additions and 1 deletions
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64
academic/ugene/hmmer3.patch Normal file
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@ -0,0 +1,64 @@
diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
index b458c12..23fa49b 100644
--- a/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp
@@ -33,7 +33,7 @@ float infinity() {
}
bool isfin( float x ) {
- return !isnan( x ) && !isinf( x );
+ return !std::isnan( x ) && !std::isinf( x );
}
const char TERM_SYM = '\0';
diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
index 9050f1c..6032970 100644
--- a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
@@ -134,7 +134,7 @@ p7_Decoding(const P7_OPROFILE *om, const P7_OMX *oxf, P7_OMX *oxb, P7_OMX *pp)
if (oxb->has_own_scales) scaleproduct *= oxf->xmx[i*p7X_NXCELLS+p7X_SCALE] / oxb->xmx[i*p7X_NXCELLS+p7X_SCALE];
}
- if (isinf(scaleproduct)) return eslERANGE;
+ if (std::isinf(scaleproduct)) return eslERANGE;
else return eslOK;
}
@@ -188,7 +188,7 @@ p7_DomainDecoding(const P7_OPROFILE *om, const P7_OMX *oxf, const P7_OMX *oxb, P
}
ddef->L = oxf->L;
- if (isinf(scaleproduct)) return eslERANGE;
+ if (std::isinf(scaleproduct)) return eslERANGE;
else return eslOK;
}
/*------------------ end, posterior decoding --------------------*/
diff --git a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
index 5bafaa4..413a6fe 100644
--- a/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
+++ b/src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/fwdback.cpp
@@ -465,9 +465,9 @@ forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7
/* On an underflow (which shouldn't happen), we counterintuitively return infinity:
* the effect of this is to force the caller to rescore us with full range.
*/
- if (isnan(xC)) ESL_EXCEPTION(eslERANGE, "forward score is NaN");
+ if (std::isnan(xC)) ESL_EXCEPTION(eslERANGE, "forward score is NaN");
else if (L>0 && xC == 0.0) ESL_EXCEPTION(eslERANGE, "forward score underflow (is 0.0)");
- else if (isinf(xC) == 1) ESL_EXCEPTION(eslERANGE, "forward score overflow (is infinity)");
+ else if (std::isinf(xC) == 1) ESL_EXCEPTION(eslERANGE, "forward score overflow (is infinity)");
if (opt_sc != NULL) *opt_sc = ox->totscale + log((double)(xC * om->xf[p7O_C][p7O_MOVE]));
return eslOK;
@@ -742,9 +742,9 @@ backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, c
if (bck->debugging) p7_omx_DumpFBRow(bck, TRUE, 0, 9, 4, bck->xmx[p7X_E], bck->xmx[p7X_N], bck->xmx[p7X_J], bck->xmx[p7X_B], bck->xmx[p7X_C]); /* logify=TRUE, <rowi>=0, width=9, precision=4*/
#endif
- if (isnan(xN)) ESL_EXCEPTION(eslERANGE, "backward score is NaN");
+ if (std::isnan(xN)) ESL_EXCEPTION(eslERANGE, "backward score is NaN");
else if (L>0 && xN == 0.0) ESL_EXCEPTION(eslERANGE, "backward score underflow (is 0.0)");
- else if (isinf(xN) == 1) ESL_EXCEPTION(eslERANGE, "backward score overflow (is infinity)");
+ else if (std::isinf(xN) == 1) ESL_EXCEPTION(eslERANGE, "backward score overflow (is infinity)");
if (opt_sc != NULL) *opt_sc = bck->totscale + log((double)xN);
return eslOK;

2
academic/ugene/ugene.SlackBuild
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@ -77,6 +77,8 @@ find -L . \
sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
sed -i "s:/share/man:/man:g" src/ugene_globals.pri
patch -p1 < $CWD/hmmer3.patch
qmake-qt5 $QMAKECONFIG -r \
QMAKE_CFLAGS="$SLKCFLAGS" \
QMAKE_CXXFLAGS="$SLKCFLAGS"

2
academic/ugene/ugene.info
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@ -5,6 +5,6 @@ DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/ugene/ugene-1.22.0.ta
MD5SUM="c876d46c75628a96ee1be5ae86b33b9c"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="qt5 libxkbcommon"
REQUIRES="qt5-webkit"
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"