diff options
| -rw-r--r-- | .SRCINFO | 4 | ||||
| -rw-r--r-- | PKGBUILD | 10 | ||||
| -rw-r--r-- | hmmer3.patch | 63 |
3 files changed, 74 insertions, 3 deletions
@@ -1,5 +1,5 @@ # Generated by mksrcinfo v8 -# Mon Apr 11 14:08:02 UTC 2016 +# Thu Apr 14 11:45:19 UTC 2016 pkgbase = ugene pkgdesc = A free cross-platform genome analysis suite. pkgver = 1.22.0 @@ -20,7 +20,9 @@ pkgbase = ugene depends = qt5-svg depends = qt5-script source = http://ugene.net/downloads/ugene-1.22.0.tar.gz + source = hmmer3.patch sha256sums = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6 + sha256sums = 57ecbaec5b5d26382d06b73ad0d599f7b07237de6ebf1e175fe662884e585736 pkgname = ugene @@ -10,10 +10,16 @@ url="http://ugene.net/" license=('GPL') depends=('qt5-base' 'libxtst' 'glu' 'qtwebkit' 'desktop-file-utils' 'procps-ng' 'python' 'shared-mime-info' 'qt5-svg' 'qt5-script') -source=(${url}downloads/$pkgname-$pkgver.tar.gz) -sha256sums=('ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6') +source=("${url}downloads/$pkgname-$pkgver.tar.gz" 'hmmer3.patch') +sha256sums=('ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6' + '57ecbaec5b5d26382d06b73ad0d599f7b07237de6ebf1e175fe662884e585736') install=$pkgname.install +prepare() { + cd "$srcdir/$pkgname-$pkgver" + patch -p1 -i "$srcdir"/hmmer3.patch +} + build() { cd "$srcdir/$pkgname-$pkgver" if [[ $CARCH == "i686" ]] diff --git a/hmmer3.patch b/hmmer3.patch new file mode 100644 index 000000000000..f3fe8615b09f --- /dev/null +++ b/hmmer3.patch @@ -0,0 +1,63 @@ +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; |