diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/ugene/hmmer3.patch | 64 | ||||
| -rw-r--r-- | academic/ugene/ugene.SlackBuild | 2 | ||||
| -rw-r--r-- | academic/ugene/ugene.info | 2 |
3 files changed, 67 insertions, 1 deletions
diff --git a/academic/ugene/hmmer3.patch b/academic/ugene/hmmer3.patch new file mode 100644 index 0000000000..9a91c068a2 --- /dev/null +++ b/academic/ugene/hmmer3.patch @@ -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; + diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index 91d53b0ec7..1013d5583b 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -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" diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index 4ccb5b9d59..0f66ab8ead 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -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" |