[Genabel-commits] r636 - in pkg/GenABEL: . R src src/GAlib src/ITERlib
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 7 20:30:10 CET 2011
Author: yurii
Date: 2011-02-07 20:30:09 +0100 (Mon, 07 Feb 2011)
New Revision: 636
Added:
pkg/GenABEL/src/GAlib/gwaa_cpp.cpp
pkg/GenABEL/src/GAlib/gwaa_cpp.h
Removed:
pkg/GenABEL/src/GAlib/gwaa_cpp.cpp
pkg/GenABEL/src/GAlib/gwaa_cpp.h
Modified:
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/GenABEL-package.R
pkg/GenABEL/src/ITERlib/iterator_functions.cpp
pkg/GenABEL/src/Makevars
pkg/GenABEL/src/Makevars.win
pkg/GenABEL/src/Makevars_distrib
Log:
dealing with compile problems before submission to CRAN
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/DESCRIPTION 2011-02-07 19:30:09 UTC (rev 636)
@@ -3,7 +3,7 @@
Title: genome-wide SNP association analysis
Version: 1.6-5
Date: 2011-02-07
-Author: Yurii Aulchenko, Maksim Struchalin
+Author: Yurii Aulchenko, Maksim Struchalin, et al.
Maintainer: Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
Depends: R (>= 2.10.0), methods, MASS
Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0)
Modified: pkg/GenABEL/R/GenABEL-package.R
===================================================================
--- pkg/GenABEL/R/GenABEL-package.R 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/R/GenABEL-package.R 2011-02-07 19:30:09 UTC (rev 636)
@@ -133,7 +133,8 @@
#'
#' @aliases GenABEL-package GenABEL
#'
-#' @author Yurii Aulchenko
+#' @author Yurii Aulchenko et al.
+#' (see help pages for specific functions)
#'
#' @references
#' If you use GenABEL package in your analysis, please cite the following work:
Deleted: pkg/GenABEL/src/GAlib/gwaa_cpp.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa_cpp.cpp 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/GAlib/gwaa_cpp.cpp 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,201 +0,0 @@
-#include "gwaa_cpp.h"
-
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
- /*
-// This code implements an exact SNP test of Hardy-Weinberg Equilibrium as described in
-// Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of
-// Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76: 000 - 000
-
-//
-// Written by Jan Wigginton
- */
-
- double SNPHWE(int obs_hets, int obs_hom1, int obs_hom2)
- {
- if (obs_hom1 < 0 || obs_hom2 < 0 || obs_hets < 0)
- {
- printf("FATAL ERROR - SNP-HWE: Current genotype configuration (%d %d %d ) includes a"
- " negative count", obs_hets, obs_hom1, obs_hom2);
- exit(EXIT_FAILURE);
- }
-
- int obs_homc = obs_hom1 < obs_hom2 ? obs_hom2 : obs_hom1;
- int obs_homr = obs_hom1 < obs_hom2 ? obs_hom1 : obs_hom2;
-
- int rare_copies = 2 * obs_homr + obs_hets;
- int genotypes = obs_hets + obs_homc + obs_homr;
-
- double * het_probs = (double *) malloc((size_t) (rare_copies + 1) * sizeof(double));
- if (het_probs == NULL)
- {
- printf("FATAL ERROR - SNP-HWE: Unable to allocate array for heterozygote probabilities" );
- exit(EXIT_FAILURE);
- }
-
- int i;
- for (i = 0; i <= rare_copies; i++)
- het_probs[i] = 0.0;
-
- /* start at midpoint */
- int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes);
-
- /* check to ensure that midpoint and rare alleles have same parity */
- if ((rare_copies & 1) ^ (mid & 1))
- mid++;
-
- int curr_hets = mid;
- int curr_homr = (rare_copies - mid) / 2;
- int curr_homc = genotypes - curr_hets - curr_homr;
-
- het_probs[mid] = 1.0;
- double sum = het_probs[mid];
- for (curr_hets = mid; curr_hets > 1; curr_hets -= 2)
- {
- het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0)
- / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0));
- sum += het_probs[curr_hets - 2];
-
- /* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */
- curr_homr++;
- curr_homc++;
- }
-
- curr_hets = mid;
- curr_homr = (rare_copies - mid) / 2;
- curr_homc = genotypes - curr_hets - curr_homr;
- for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2)
- {
- het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc
- /((curr_hets + 2.0) * (curr_hets + 1.0));
- sum += het_probs[curr_hets + 2];
-
- /* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */
- curr_homr--;
- curr_homc--;
- }
-
- for (i = 0; i <= rare_copies; i++)
- het_probs[i] /= sum;
-
- /* alternate p-value calculation for p_hi/p_lo
- double p_hi = het_probs[obs_hets];
- for (i = obs_hets + 1; i <= rare_copies; i++)
- p_hi += het_probs[i];
-
- double p_lo = het_probs[obs_hets];
- for (i = obs_hets - 1; i >= 0; i--)
- p_lo += het_probs[i];
-
-
- double p_hi_lo = p_hi < p_lo ? 2.0 * p_hi : 2.0 * p_lo;
- */
-
- double p_hwe = 0.0;
- /* p-value calculation for p_hwe */
- for (i = 0; i <= rare_copies; i++)
- {
- if (het_probs[i] > het_probs[obs_hets])
- continue;
- p_hwe += het_probs[i];
- }
-
- p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe;
-
- free(het_probs);
-
- return p_hwe;
- }
-
-
- void snp_summary_exhweWrapper(double *indata, unsigned long int indataHeight,
- unsigned long int indataWidth, double *outdata,
- unsigned long int &outdataNcol, unsigned long int &outdataNrow,
- unsigned int narg, SEXP *argList)
- {
- //Rprintf("indataHeight=%d\n",indataHeight);
- //Rprintf("indataWidth=%d\n",indataWidth);
- unsigned int gt[indataHeight];
- if (indata) {
- unsigned int i;
- for(i=0;i<indataHeight*indataWidth;i++) {
- if (isnan(indata[i])) gt[i] = 0;
- else gt[i] = 1 + (unsigned int) indata[i];
- //Rprintf(" %f %d;",indata[i],gt[i]);
- }
- //Rprintf("\n");
-
- unsigned int nids = indataHeight*indataWidth;
-
- //Rprintf("nids=%d\n",nids);
- snp_summary_exhwe_Processor(gt, nids, outdata);
- //for (int i=0;i<9;i++) Rprintf(" %f",outdata[i]); Rprintf("\n");
- } else {
- outdataNcol = 9;
- outdataNrow = 1;
- }
- }
-
- void snp_summary_exhwe_Processor(unsigned int *gt, unsigned int nids, double *out) {
- unsigned int i,j,idx;
- //unsigned int nids = (*Nids);
- char str;
- unsigned int count[3];
- double meaids,p,pmax,qmax,maf,fmax,loglik0,loglik1,chi2lrt;
- count[0]=count[1]=count[2]=0;
- p = 0.;
- for (i=0;i<9;i++) out[i] = 0.;
- for (i=0;i<nids;i++)
- if (gt[i]) {
- count[gt[i]-1]++;
- p+=(gt[i]-1);
- }
-
- meaids = 1.*(count[0]+count[1]+count[2]);
- out[0] = meaids;
- out[1] = meaids/nids;
- if (meaids>0)
- out[2] = p/(2.*meaids);
- else
- out[2] = 0.0;
- out[3] = count[0];
- out[4] = count[1];
- out[5] = count[2];
- if (meaids>0) {
- out[6] = SNPHWE(count[1],count[0],count[2]);
- pmax = out[2];
- qmax = 1.-pmax;
- maf = qmax; if (pmax<qmax) maf = pmax;
- if (maf>1.e-16) {
- fmax = (4.*count[0]*count[2] - 1.*count[1]*count[1])/((2.*count[0]+1.*count[1])*(2.*count[2]+1.*count[1]));
- loglik0 = 0.;
- if (count[0]) loglik0 += 2.*count[0]*log(qmax);
- if (count[1]) loglik0 += 1.*count[1]*log(2.*qmax*pmax);
- if (count[2]) loglik0 += 2.*count[2]*log(pmax);
- loglik1 = 0.;
- if (count[0]) loglik1 += 1.*count[0]*log(qmax*qmax+qmax*pmax*fmax);
- if (count[1]) loglik1 += 1.*count[1]*log(2.*qmax*pmax*(1.-fmax));
- if (count[2]) loglik1 += 1.*count[2]*log(pmax*pmax+qmax*pmax*fmax);
- chi2lrt = 2*(loglik1-loglik0);
- out[7] = fmax;
- out[8] = chi2lrt;
- } else {
- out[7] = 0.;//maf;
- out[8] = 0.;
- }
- } else {
- out[6] = 1.0;
- }
-
- }
-
-
-#ifdef __cplusplus
-}
-#endif
-
Copied: pkg/GenABEL/src/GAlib/gwaa_cpp.cpp (from rev 620, pkg/GenABEL/src/GAlib/gwaa_cpp.cpp)
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa_cpp.cpp (rev 0)
+++ pkg/GenABEL/src/GAlib/gwaa_cpp.cpp 2011-02-07 19:30:09 UTC (rev 636)
@@ -0,0 +1,208 @@
+#include <new>
+#include "gwaa_cpp.h"
+
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+ /*
+// This code implements an exact SNP test of Hardy-Weinberg Equilibrium as described in
+// Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of
+// Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76: 000 - 000
+
+//
+// Written by Jan Wigginton
+ */
+
+ double SNPHWE(int obs_hets, int obs_hom1, int obs_hom2)
+ {
+ if (obs_hom1 < 0 || obs_hom2 < 0 || obs_hets < 0)
+ {
+ printf("FATAL ERROR - SNP-HWE: Current genotype configuration (%d %d %d ) includes a"
+ " negative count", obs_hets, obs_hom1, obs_hom2);
+ exit(EXIT_FAILURE);
+ }
+
+ int obs_homc = obs_hom1 < obs_hom2 ? obs_hom2 : obs_hom1;
+ int obs_homr = obs_hom1 < obs_hom2 ? obs_hom1 : obs_hom2;
+
+ int rare_copies = 2 * obs_homr + obs_hets;
+ int genotypes = obs_hets + obs_homc + obs_homr;
+
+ double * het_probs = (double *) malloc((size_t) (rare_copies + 1) * sizeof(double));
+ if (het_probs == NULL)
+ {
+ printf("FATAL ERROR - SNP-HWE: Unable to allocate array for heterozygote probabilities" );
+ exit(EXIT_FAILURE);
+ }
+
+ int i;
+ for (i = 0; i <= rare_copies; i++)
+ het_probs[i] = 0.0;
+
+ /* start at midpoint */
+ int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes);
+
+ /* check to ensure that midpoint and rare alleles have same parity */
+ if ((rare_copies & 1) ^ (mid & 1))
+ mid++;
+
+ int curr_hets = mid;
+ int curr_homr = (rare_copies - mid) / 2;
+ int curr_homc = genotypes - curr_hets - curr_homr;
+
+ het_probs[mid] = 1.0;
+ double sum = het_probs[mid];
+ for (curr_hets = mid; curr_hets > 1; curr_hets -= 2)
+ {
+ het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0)
+ / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0));
+ sum += het_probs[curr_hets - 2];
+
+ /* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */
+ curr_homr++;
+ curr_homc++;
+ }
+
+ curr_hets = mid;
+ curr_homr = (rare_copies - mid) / 2;
+ curr_homc = genotypes - curr_hets - curr_homr;
+ for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2)
+ {
+ het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc
+ /((curr_hets + 2.0) * (curr_hets + 1.0));
+ sum += het_probs[curr_hets + 2];
+
+ /* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */
+ curr_homr--;
+ curr_homc--;
+ }
+
+ for (i = 0; i <= rare_copies; i++)
+ het_probs[i] /= sum;
+
+ /* alternate p-value calculation for p_hi/p_lo
+ double p_hi = het_probs[obs_hets];
+ for (i = obs_hets + 1; i <= rare_copies; i++)
+ p_hi += het_probs[i];
+
+ double p_lo = het_probs[obs_hets];
+ for (i = obs_hets - 1; i >= 0; i--)
+ p_lo += het_probs[i];
+
+
+ double p_hi_lo = p_hi < p_lo ? 2.0 * p_hi : 2.0 * p_lo;
+ */
+
+ double p_hwe = 0.0;
+ /* p-value calculation for p_hwe */
+ for (i = 0; i <= rare_copies; i++)
+ {
+ if (het_probs[i] > het_probs[obs_hets])
+ continue;
+ p_hwe += het_probs[i];
+ }
+
+ p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe;
+
+ free(het_probs);
+
+ return p_hwe;
+ }
+
+
+ void snp_summary_exhweWrapper(double *indata, unsigned long int indataHeight,
+ unsigned long int indataWidth, double *outdata,
+ unsigned long int &outdataNcol, unsigned long int &outdataNrow,
+ unsigned int narg, SEXP *argList)
+ {
+ //Rprintf("indataHeight=%d\n",indataHeight);
+ //Rprintf("indataWidth=%d\n",indataWidth);
+ //unsigned int gt[indataHeight];
+ unsigned int * gt = new (std::nothrow) unsigned int [indataHeight];
+ if (gt == NULL) {
+ Rprintf("cannot get RAM for gt\n");
+ return;
+ }
+ if (indata) {
+ unsigned int i;
+ for(i=0;i<indataHeight*indataWidth;i++) {
+ if (isnan(indata[i])) gt[i] = 0;
+ else gt[i] = 1 + (unsigned int) indata[i];
+ //Rprintf(" %f %d;",indata[i],gt[i]);
+ }
+ //Rprintf("\n");
+
+ unsigned int nids = indataHeight*indataWidth;
+
+ //Rprintf("nids=%d\n",nids);
+ snp_summary_exhwe_Processor(gt, nids, outdata);
+ //for (int i=0;i<9;i++) Rprintf(" %f",outdata[i]); Rprintf("\n");
+ } else {
+ outdataNcol = 9;
+ outdataNrow = 1;
+ }
+ delete [] gt;
+ }
+
+ void snp_summary_exhwe_Processor(unsigned int *gt, unsigned int nids, double *out) {
+ unsigned int i; //,j,idx;
+ //unsigned int nids = (*Nids);
+ //char str;
+ unsigned int count[3];
+ double meaids,p,pmax,qmax,maf,fmax,loglik0,loglik1,chi2lrt;
+ count[0]=count[1]=count[2]=0;
+ p = 0.;
+ for (i=0;i<9;i++) out[i] = 0.;
+ for (i=0;i<nids;i++)
+ if (gt[i]) {
+ count[gt[i]-1]++;
+ p+=(gt[i]-1);
+ }
+
+ meaids = 1.*(count[0]+count[1]+count[2]);
+ out[0] = meaids;
+ out[1] = meaids/nids;
+ if (meaids>0)
+ out[2] = p/(2.*meaids);
+ else
+ out[2] = 0.0;
+ out[3] = count[0];
+ out[4] = count[1];
+ out[5] = count[2];
+ if (meaids>0) {
+ out[6] = SNPHWE(count[1],count[0],count[2]);
+ pmax = out[2];
+ qmax = 1.-pmax;
+ maf = qmax; if (pmax<qmax) maf = pmax;
+ if (maf>1.e-16) {
+ fmax = (4.*count[0]*count[2] - 1.*count[1]*count[1])/((2.*count[0]+1.*count[1])*(2.*count[2]+1.*count[1]));
+ loglik0 = 0.;
+ if (count[0]) loglik0 += 2.*count[0]*log(qmax);
+ if (count[1]) loglik0 += 1.*count[1]*log(2.*qmax*pmax);
+ if (count[2]) loglik0 += 2.*count[2]*log(pmax);
+ loglik1 = 0.;
+ if (count[0]) loglik1 += 1.*count[0]*log(qmax*qmax+qmax*pmax*fmax);
+ if (count[1]) loglik1 += 1.*count[1]*log(2.*qmax*pmax*(1.-fmax));
+ if (count[2]) loglik1 += 1.*count[2]*log(pmax*pmax+qmax*pmax*fmax);
+ chi2lrt = 2*(loglik1-loglik0);
+ out[7] = fmax;
+ out[8] = chi2lrt;
+ } else {
+ out[7] = 0.;//maf;
+ out[8] = 0.;
+ }
+ } else {
+ out[6] = 1.0;
+ }
+
+ }
+
+
+#ifdef __cplusplus
+}
+#endif
+
Deleted: pkg/GenABEL/src/GAlib/gwaa_cpp.h
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa_cpp.h 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/GAlib/gwaa_cpp.h 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,23 +0,0 @@
-#include <R.h>
-#include <Rinternals.h>
-
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-
-void snp_summary_exhweWrapper(double *indata, unsigned long int indataHeight,
- unsigned long int indataWidth, double *outdata,
- unsigned long int &outdataNcol, unsigned long int &outdataNrow, unsigned int narg,
- SEXP *argList);
-
-void snp_summary_exhwe_Processor(unsigned int *gt, unsigned int nids, double *out);
-
-
-#ifdef __cplusplus
-}
-#endif
-
Copied: pkg/GenABEL/src/GAlib/gwaa_cpp.h (from rev 620, pkg/GenABEL/src/GAlib/gwaa_cpp.h)
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa_cpp.h (rev 0)
+++ pkg/GenABEL/src/GAlib/gwaa_cpp.h 2011-02-07 19:30:09 UTC (rev 636)
@@ -0,0 +1,23 @@
+#include <R.h>
+#include <Rinternals.h>
+
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+
+void snp_summary_exhweWrapper(double *indata, unsigned long int indataHeight,
+ unsigned long int indataWidth, double *outdata,
+ unsigned long int &outdataNcol, unsigned long int &outdataNrow, unsigned int narg,
+ SEXP *argList);
+
+void snp_summary_exhwe_Processor(unsigned int *gt, unsigned int nids, double *out);
+
+
+#ifdef __cplusplus
+}
+#endif
+
Modified: pkg/GenABEL/src/ITERlib/iterator_functions.cpp
===================================================================
--- pkg/GenABEL/src/ITERlib/iterator_functions.cpp 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/ITERlib/iterator_functions.cpp 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,3 +1,4 @@
+#include <new>
#include "Rstaff.h"
#include "iterator_functions.h"
@@ -103,9 +104,20 @@
int i, j, cstr, igt, i1=1;
int nbytes;
int dgt;
- double Ttotg, mx, bb, totg[nstra], x2[nstra], sumx[nstra];
- double Tsg0, Tsg1, Tsg2, sg0[nstra], sg1[nstra], sg2[nstra], xg0[nstra], xg1[nstra], xg2[nstra];
+ double Ttotg, mx, bb;
+ double Tsg0, Tsg1, Tsg2;
double u, v, u0, u1, u2, m0, m1, m2, v00, v02, v11, v12, v22, det;
+
+ double * totg = new (std::nothrow) double [nstra];if (totg == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * x2 = new (std::nothrow) double [nstra];if (x2 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * sumx = new (std::nothrow) double [nstra];if (sumx == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * sg0 = new (std::nothrow) double [nstra];if (sg0 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * sg1 = new (std::nothrow) double [nstra];if (sg1 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * sg2 = new (std::nothrow) double [nstra];if (sg2 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * xg0 = new (std::nothrow) double [nstra];if (xg0 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * xg1 = new (std::nothrow) double [nstra];if (xg1 == NULL) {Rprintf("cannot allocate RAM");return;}
+ double * xg2 = new (std::nothrow) double [nstra];if (xg2 == NULL) {Rprintf("cannot allocate RAM");return;}
+
mx = -999.99;
if ((nids % 4) == 0) nbytes = nids/4; else nbytes = ceil(1.*nids/4.);
// char chgt[nbytes];
@@ -253,6 +265,17 @@
chi2[igt+2*nsnps] = 1.;
// }
}
+
+ delete [] totg;
+ delete [] x2;
+ delete [] sumx;
+ delete [] sg0;
+ delete [] sg1;
+ delete [] sg2;
+ delete [] xg0;
+ delete [] xg1;
+ delete [] xg2;
+
}
#ifdef __cplusplus
Modified: pkg/GenABEL/src/Makevars
===================================================================
--- pkg/GenABEL/src/Makevars 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/Makevars 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,4 +1,4 @@
-PKG_CXXFLAGS=-DCOMPILE_WITH_R
+PKG_CXXFLAGS=-DCOMPILE_WITH_R -Wall -pedantic
all: $(SHLIB) cleanNoSo
Modified: pkg/GenABEL/src/Makevars.win
===================================================================
--- pkg/GenABEL/src/Makevars.win 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/Makevars.win 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,2 +1,2 @@
-PKG_CXXFLAGS=-DCOMPILE_WITH_R
+PKG_CXXFLAGS=-DCOMPILE_WITH_R -Wall -pedantic
Modified: pkg/GenABEL/src/Makevars_distrib
===================================================================
--- pkg/GenABEL/src/Makevars_distrib 2011-02-07 08:55:47 UTC (rev 635)
+++ pkg/GenABEL/src/Makevars_distrib 2011-02-07 19:30:09 UTC (rev 636)
@@ -1,2 +1,2 @@
-PKG_CXXFLAGS=-DCOMPILE_WITH_R
+PKG_CXXFLAGS=-DCOMPILE_WITH_R -Wall -pedantic
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