commit: f457d5639ad562f52d697a2b33a7474a8c76d0a2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed Oct 28 09:06:45 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Oct 28 09:06:56 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f457d563
sci-chemistry/ambertools: Fix for gcc-5 and format-security Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-chemistry/ambertools/ambertools-12_p38.ebuild | 16 ++-- .../files/ambertools-12_p38-format-security.patch | 100 +++++++++++++++++++++ .../ambertools/files/ambertools-12_p38-gcc5.patch | 28 ++++++ 3 files changed, 136 insertions(+), 8 deletions(-) diff --git a/sci-chemistry/ambertools/ambertools-12_p38.ebuild b/sci-chemistry/ambertools/ambertools-12_p38.ebuild index 812bbdb..1c907c4 100644 --- a/sci-chemistry/ambertools/ambertools-12_p38.ebuild +++ b/sci-chemistry/ambertools/ambertools-12_p38.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ EAPI=5 -inherit eutils fortran-2 multilib toolchain-funcs +inherit eutils fortran-2 multilib multiprocessing toolchain-funcs DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" HOMEPAGE="http://ambermd.org/#AmberTools"; @@ -54,6 +54,8 @@ pkg_setup() { src_prepare() { epatch \ + "${FILESDIR}"/${P}-gcc5.patch \ + "${FILESDIR}"/${P}-format-security.patch \ "${FILESDIR}"/${PN}-12-gentoo.patch \ "${WORKDIR}"/bugfixes/bugfix.{14..38} cd "${S}"/AmberTools/src || die @@ -69,9 +71,7 @@ src_prepare() { reduce \ ucpp-1.3 \ || die -} -src_configure() { cd "${S}"/AmberTools/src || die sed \ -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ @@ -94,6 +94,9 @@ src_configure() { -e "s:arsecond_:arscnd_:g" \ -i sff/time.c sff/sff.h sff/sff.c || die +} + +src_configure() { local myconf="--no-updates" use X || myconf="${myconf} -noX11" @@ -114,10 +117,7 @@ src_configure() { } src_test() { - # Get the number of physical cores - local ncpus=$(grep "^core id" /proc/cpuinfo | sort -u | wc -l) - # Limit number of OpenMP threads - use openmp && export OMP_NUM_THREADS=$((1+${ncpus}/2)) + use openmp && export OMP_NUM_THREADS=$(makeopts_jobs) emake test } diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch new file mode 100644 index 0000000..bb22a62 --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch @@ -0,0 +1,100 @@ + AmberTools/src/mdgx/ChargeFit.c | 4 ++-- + AmberTools/src/nab/cgen.c | 2 +- + AmberTools/src/nab/traceback.c | 2 +- + AmberTools/src/ptraj/cluster.c | 2 +- + AmberTools/src/ptraj/interface.c | 6 +++--- + AmberTools/src/semantics/parse.c | 2 +- + 6 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/AmberTools/src/mdgx/ChargeFit.c b/AmberTools/src/mdgx/ChargeFit.c +index fccf5d0..fe4afac 100644 +--- a/AmberTools/src/mdgx/ChargeFit.c ++++ b/AmberTools/src/mdgx/ChargeFit.c +@@ -77,9 +77,9 @@ static void AssignGridTopologies(fset *myfit, prmtop *tp) + } + for (i = 0; i < myfit->ngrd; i++) { + if (myfit->tpname.map[i][0] == '\0') { +- sprintf(myfit->tpname.map[i], tp->source); ++ sprintf(myfit->tpname.map[i], "%s", tp->source); + if (myfit->eprule.map[i][0] == '\0' && tp->eprulesource[0] != '\0') { +- sprintf(myfit->eprule.map[i], tp->eprulesource); ++ sprintf(myfit->eprule.map[i], "%s", tp->eprulesource); + } + } + } +diff --git a/AmberTools/src/nab/cgen.c b/AmberTools/src/nab/cgen.c +index 6254d44..e206879 100644 +--- a/AmberTools/src/nab/cgen.c ++++ b/AmberTools/src/nab/cgen.c +@@ -1642,7 +1642,7 @@ static char *CG_gentype( char *csp, NODE_T *npt ) + strcpy( csp, tname ); + csp += strlen( csp ); + }else +- fprintf( cg_cfp, tname ); ++ fprintf( cg_cfp, "%s", tname ); + needspace = TRUE; + return( csp ); + } +diff --git a/AmberTools/src/nab/traceback.c b/AmberTools/src/nab/traceback.c +index f916474..e376552 100644 +--- a/AmberTools/src/nab/traceback.c ++++ b/AmberTools/src/nab/traceback.c +@@ -6,7 +6,7 @@ + int rt_errormsg( int fatal, char msg[] ) + { + +- fprintf( stderr, msg ); ++ fprintf( stderr, "%s", msg ); + if( fatal ) + exit( 1 ); + return(0); +diff --git a/AmberTools/src/ptraj/cluster.c b/AmberTools/src/ptraj/cluster.c +index 2cb60f0..5e0f33d 100644 +--- a/AmberTools/src/ptraj/cluster.c ++++ b/AmberTools/src/ptraj/cluster.c +@@ -1240,7 +1240,7 @@ void ClusteringMergeNames(PtrajClustering* This, ClusterNode* MergeNodeA, Cluste + { + return; + } +- sprintf(Temp, ClusterB->Name); ++ sprintf(Temp, "%s", ClusterB->Name); + sprintf(ClusterB->Name, "(%s,%s)", ClusterA->Name, Temp); + + } +diff --git a/AmberTools/src/ptraj/interface.c b/AmberTools/src/ptraj/interface.c +index 4087fa7..1ee4273 100644 +--- a/AmberTools/src/ptraj/interface.c ++++ b/AmberTools/src/ptraj/interface.c +@@ -97,8 +97,8 @@ interface(interfaceMode mode, char *filename) + + tokenlist = (Token *) &rdparmTokenlist; + +- fprintf(stdout, rdparm_header); +- fprintf(stdout, rdparm_prompt); ++ fprintf(stdout, "%s", rdparm_header); ++ fprintf(stdout, "%s", rdparm_prompt); + while (1) { + + fflush(stdout); +@@ -112,7 +112,7 @@ interface(interfaceMode mode, char *filename) + + } + +- fprintf(stdout, rdparm_prompt); ++ fprintf(stdout, "%s", rdparm_prompt); + } + } + } +diff --git a/AmberTools/src/semantics/parse.c b/AmberTools/src/semantics/parse.c +index 55c724c..68f23da 100644 +--- a/AmberTools/src/semantics/parse.c ++++ b/AmberTools/src/semantics/parse.c +@@ -2039,7 +2039,7 @@ int n_tab; + DEF_T tab[]; + { + +- fprintf( fp, oval ); ++ fprintf( fp, "%s", oval ); + + } + diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch new file mode 100644 index 0000000..92e6495 --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch @@ -0,0 +1,28 @@ + AmberTools/src/configure2 | 14 ++++++++------ + 1 file changed, 8 insertions(+), 6 deletions(-) + +diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2 +index 913c50d..1232f6a 100755 +--- a/AmberTools/src/configure2 ++++ b/AmberTools/src/configure2 +@@ -703,12 +703,14 @@ gnu) + # if gcc <= 4.2, fftw3 is not compiled and pbsa fft solver and rism + # are disabled + if [ "$rism" != 'no' -o -n "$pbsaflag" ]; then +- if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \ +- || [ $gnu_majorversion -le 3 ]; then +- echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler." +- echo " Please re-run configure with the '-nofftw3' flag to use this compiler:" +- echo " `mod_command_args '-rism' '-nofftw3'`" +- exit 1 ++ if [ $gnu_majorversion -lt 5 ]; then ++ if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \ ++ || [ $gnu_majorversion -le 3 ]; then ++ echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler." ++ echo " Please re-run configure with the '-nofftw3' flag to use this compiler:" ++ echo " `mod_command_args '-rism' '-nofftw3'`" ++ exit 1 ++ fi + fi + fi +
