1 files changed, 0 insertions, 64 deletions
diff --git a/academic/ugene/hmmer3.patch b/academic/ugene/hmmer3.patch
deleted file mode 100644
index 9a91c068a2..0000000000
--- a/academic/ugene/hmmer3.patch
+++ /dev/null
@@ -1,64 +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;
-