diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-06-25 12:04:05 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-06-29 12:54:48 +0200 |
| commit | cc6ed477372f8cb3aeb579fa6a5858179548f9ba (patch) | |
| tree | 12c93a644b1f88942f1c9676bc6d6c3d563bf3f5 /gnu/packages/patches | |
| parent | 5c852e085d4e6f063f70109aaecd3f91a5f8fee5 (diff) | |
gnu: Add plink.
* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/plink-1.07-unclobber-i.patch | 69 |
1 files changed, 69 insertions, 0 deletions
diff --git a/gnu/packages/patches/plink-1.07-unclobber-i.patch b/gnu/packages/patches/plink-1.07-unclobber-i.patch new file mode 100644 index 0000000000..60cd97ba4a --- /dev/null +++ b/gnu/packages/patches/plink-1.07-unclobber-i.patch @@ -0,0 +1,69 @@ +GCC rightfully complains about redefined variables, as iterator declarations +appear inside loops with a loop variable of the same name. + +This patch has been sent upstream. + +--- a/sets.cpp 2015-06-25 11:22:08.252821681 +0200 ++++ b/sets.cpp 2015-06-25 11:22:23.239187985 +0200 +@@ -768,11 +768,11 @@ + ////////////////////////////////////////////// + // Reset original missing status + +- vector<Individual*>::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector<Individual*>::iterator it = PP->sample.begin(); ++ while ( it != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*it)->missing = (*it)->flag; ++ ++it; + } + + //////////////////////////////////////////////// + +--- a/elf.cpp 2009-10-10 18:00:21.000000000 +0200 ++++ b/elf.cpp 2015-06-25 11:34:06.136835756 +0200 +@@ -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 it = chr_cnt.begin(); ++ while ( it != chr_cnt.end() ) + { +- int c = i->first; ++ int c = it->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; ++ ++it; + } + + } + +--- plink-1.07-src/idhelp.cpp 2009-10-10 18:00:22.000000000 +0200 ++++ plink-1.07-src/idhelp.cpp.patched 2015-06-25 11:37:39.387204086 +0200 +@@ -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 jit = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( jit != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*jit)->name + " " ); ++ ++jit; + } + PP->printLOG(" }"); + } |