diff options
| author | Gerald Pfeifer <gerald@FreeBSD.org> | 2013-12-13 09:34:40 +0000 |
|---|---|---|
| committer | Gerald Pfeifer <gerald@FreeBSD.org> | 2013-12-13 09:34:40 +0000 |
| commit | 2291db64eca37ef1d8fc4d018c7dd435c7171918 (patch) | |
| tree | 541897fec7d77095fda447b9828d19e0cec4f332 /biology/plink | |
| parent | 71fe78ed54d6922689eb9acb351c4f628950fe39 (diff) | |
Fix the build with more standards-compliant compilers such as GCC 4.7. [1]
On the way replace USE_GMAKE by USES=gmake.
PR: 184566 [1], 182136
Submitted by: Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by: maintainer (Jason Bacon <jwbacon@tds.net>) [1]
Notes
Notes:
svn path=/head/; revision=336328
Diffstat (limited to 'biology/plink')
| -rw-r--r-- | biology/plink/Makefile | 2 | ||||
| -rw-r--r-- | biology/plink/files/patch-elf.cpp | 25 | ||||
| -rw-r--r-- | biology/plink/files/patch-idhelp.cpp | 19 | ||||
| -rw-r--r-- | biology/plink/files/patch-sets.cpp | 18 |
4 files changed, 63 insertions, 1 deletions
diff --git a/biology/plink/Makefile b/biology/plink/Makefile index 3a03a5eee00c..bfd37ec1e825 100644 --- a/biology/plink/Makefile +++ b/biology/plink/Makefile @@ -15,8 +15,8 @@ LICENSE= GPLv2 LIB_DEPENDS= liblapack.so:${PORTSDIR}/math/lapack +USES= gmake USE_ZIP= yes -USE_GMAKE= yes USE_FORTRAN= yes # Make it use the same compiler as lapack PLIST_FILES= bin/plink diff --git a/biology/plink/files/patch-elf.cpp b/biology/plink/files/patch-elf.cpp new file mode 100644 index 000000000000..0cc22cb84e6a --- /dev/null +++ b/biology/plink/files/patch-elf.cpp @@ -0,0 +1,25 @@ +--- elf.cpp.orig 2013-11-16 17:09:56.000000000 +0100 ++++ elf.cpp 2013-11-16 17:10:24.000000000 +0100 +@@ -1175,10 +1175,10 @@ + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map<int,int>::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map<int,int>::iterator ichr = chr_cnt.begin(); ++ while ( ichr != chr_cnt.end() ) + { +- int c = i->first; ++ int c = ichr->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +@@ -1189,7 +1189,7 @@ + << setw(8) << y << " " + << setw(8) << (double)x / (double)y << "\n"; + +- ++i; ++ ++ichr; + } + + } diff --git a/biology/plink/files/patch-idhelp.cpp b/biology/plink/files/patch-idhelp.cpp new file mode 100644 index 000000000000..c0026984f854 --- /dev/null +++ b/biology/plink/files/patch-idhelp.cpp @@ -0,0 +1,19 @@ +--- idhelp.cpp.orig 2013-11-16 17:11:42.000000000 +0100 ++++ idhelp.cpp 2013-11-16 17:12:53.000000000 +0100 +@@ -772,12 +772,12 @@ + for (int j = 0 ; j < jointField.size(); j++ ) + { + set<IDField*> & jf = jointField[j]; +- set<IDField*>::iterator j = jf.begin(); ++ set<IDField*>::iterator jfit = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( jfit != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*jfit)->name + " " ); ++ ++jfit; + } + PP->printLOG(" }"); + } diff --git a/biology/plink/files/patch-sets.cpp b/biology/plink/files/patch-sets.cpp new file mode 100644 index 000000000000..4d773fb36db2 --- /dev/null +++ b/biology/plink/files/patch-sets.cpp @@ -0,0 +1,18 @@ +--- sets.cpp.orig 2013-11-16 17:06:29.000000000 +0100 ++++ sets.cpp 2013-11-16 17:07:12.000000000 +0100 +@@ -768,11 +768,11 @@ + ////////////////////////////////////////////// + // Reset original missing status + +- vector<Individual*>::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector<Individual*>::iterator ipp = PP->sample.begin(); ++ while ( ipp != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*ipp)->missing = (*ipp)->flag; ++ ++ipp; + } + + //////////////////////////////////////////////// |