diff options
| -rw-r--r-- | .SRCINFO | 12 | ||||
| -rw-r--r-- | PKGBUILD | 11 | ||||
| -rw-r--r-- | hmmer3.patch | 63 |
3 files changed, 10 insertions, 76 deletions
@@ -1,9 +1,9 @@ # Generated by mksrcinfo v8 -# Fri Jun 3 07:41:09 UTC 2016 +# Wed Aug 10 08:48:13 UTC 2016 pkgbase = ugene pkgdesc = A free cross-platform genome analysis suite. - pkgver = 1.22.0 - pkgrel = 2 + pkgver = 1.23.0 + pkgrel = 1 url = http://ugene.net/ install = ugene.install arch = i686 @@ -19,10 +19,8 @@ pkgbase = ugene depends = shared-mime-info depends = qt5-svg depends = qt5-script - source = http://ugene.net/downloads/ugene-1.22.0.tar.gz - source = hmmer3.patch - sha256sums = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6 - sha256sums = 57ecbaec5b5d26382d06b73ad0d599f7b07237de6ebf1e175fe662884e585736 + source = http://ugene.net/downloads/ugene-1.23.0.tar.gz + sha256sums = 48ab569c393ca549888a3cd13411fd6cb7d9da7e35198c37c7194132b6fd117d pkgname = ugene @@ -2,22 +2,21 @@ # Contributor: talavis <aur talavis eu> # Contributor: Bruno Vieira <mail@bmpvieira.com> pkgname=ugene -pkgver=1.22.0 -pkgrel=2 +pkgver=1.23.0 +pkgrel=1 pkgdesc="A free cross-platform genome analysis suite." arch=('i686' 'x86_64') 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-$pkgver.tar.gz" 'hmmer3.patch') -sha256sums=('ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6' - '57ecbaec5b5d26382d06b73ad0d599f7b07237de6ebf1e175fe662884e585736') +source=("${url}downloads/$pkgname-$pkgver.tar.gz") +sha256sums=('48ab569c393ca549888a3cd13411fd6cb7d9da7e35198c37c7194132b6fd117d') install=$pkgname.install prepare() { cd "$srcdir/$pkgname-$pkgver" - patch -p1 -i "$srcdir"/hmmer3.patch + #nothing for now } diff --git a/hmmer3.patch b/hmmer3.patch deleted file mode 100644 index f3fe8615b09f..000000000000 --- a/hmmer3.patch +++ /dev/null @@ -1,63 +0,0 @@ -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; |