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| author | Allen | 2018-12-18 12:00:11 +0800 |
|---|---|---|
| committer | Allen | 2018-12-18 12:02:32 +0800 |
| commit | 66bc4659079b970db5d9dfe05f63fe91065f72a7 (patch) | |
| tree | c1f656745005e11e0c9b7d02b7cf299049d710e6 | |
| parent | 8f506092f84112ba7c640498fa3e7263dff2d51d (diff) | |
| download | aur-66bc4659079b970db5d9dfe05f63fe91065f72a7.tar.gz | |
Patch PSSM.cpp to read double properly
| -rw-r--r-- | .SRCINFO | 4 | ||||
| -rw-r--r-- | PKGBUILD | 8 | ||||
| -rw-r--r-- | PSSM.cpp.patch | 34 |
3 files changed, 42 insertions, 4 deletions
@@ -1,13 +1,15 @@ pkgbase = rmotifgen pkgdesc = Random motif sequence generator for genomic sequences pkgver = 3.0 - pkgrel = 1 + pkgrel = 2 url = http://bioinformatics.louisville.edu/rMotifGen.html arch = i686 arch = x86_64 license = GPL source = http://bioinformatics.louisville.edu/localresources/software/rMotifGen3.0.tar.gz + source = PSSM.cpp.patch md5sums = b8b43a6cfd3c8ade4eee3306c9661eda + md5sums = b595210ee6873e37fcd5986866a95ba3 pkgname = rmotifgen @@ -1,20 +1,22 @@ # Maintainer: allencch <allencch at hotmail dot com> pkgname=rmotifgen pkgver=3.0 -pkgrel=1 +pkgrel=2 pkgdesc="Random motif sequence generator for genomic sequences" arch=('i686' 'x86_64') url="http://bioinformatics.louisville.edu/rMotifGen.html" license=('GPL') depends=() -source=("http://bioinformatics.louisville.edu/localresources/software/rMotifGen${pkgver}.tar.gz") -md5sums=('b8b43a6cfd3c8ade4eee3306c9661eda') +source=("http://bioinformatics.louisville.edu/localresources/software/rMotifGen${pkgver}.tar.gz" "PSSM.cpp.patch") +md5sums=('b8b43a6cfd3c8ade4eee3306c9661eda' + 'b595210ee6873e37fcd5986866a95ba3') build() { cd "${srcdir}/rMotifGen_v${pkgver}" sed -i -e '38i#include <cstring>' CommonRoutines.cpp sed -i -e 's|PAM1\.prob|/opt/rMotifGen/PAM1.prob|' SubstitutionMatrices.cpp sed -i -e '/^CCFLAGS/ s|$| -fpermissive|' Makefile + patch -u < ../PSSM.cpp.patch make } diff --git a/PSSM.cpp.patch b/PSSM.cpp.patch new file mode 100644 index 000000000000..4623d582486a --- /dev/null +++ b/PSSM.cpp.patch @@ -0,0 +1,34 @@ +--- PSSM.cpp 2007-05-31 17:36:24.000000000 +0800 ++++ PSSM.cpp 2018-12-18 11:38:35.805256544 +0800 +@@ -204,13 +204,8 @@ + string tmpS; + double tmpD; + ss >> tmpS; +- if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) { +- errorVal = 29; +- return(false); +- } +- else { +- m[i-1][j] = tmpD; +- } ++ tmpD = atof(tmpS.c_str()); ++ m[i-1][j] = tmpD; + } + } + +@@ -285,13 +280,8 @@ + + // MAKE SURE EACH COLUMN IS A POSITIVE DOUBLE VALUE + +- if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) { +- errorVal = 29; +- return(false); +- } +- else { +- m[j][i] = tmpD; +- } ++ tmpD = atof(tmpS.c_str()); ++ m[i-1][j] = tmpD; + } + } + |