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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PICS
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pics.c -o pics.o
pics.c: In function ‘iterEM’:
pics.c:581:25: warning: unused variable ‘mu’ [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0;
^˜
pics.c: In function ‘ECM1’:
pics.c:803:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(status1==0 & status2==0)
˜˜˜˜˜˜˜^˜˜
pics.c:963:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(status1==0 & status2==0)
˜˜˜˜˜˜˜^˜˜
pics.c:651:15: warning: unused variable ‘k’ [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function ‘ECM2’:
pics.c:1009:66: warning: unused variable ‘ee’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜
pics.c:1009:57: warning: unused variable ‘ggR’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜
pics.c:1009:52: warning: unused variable ‘ggF’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜
pics.c:1009:47: warning: unused variable ‘aaR’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜
pics.c:1009:42: warning: unused variable ‘aaF’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜
pics.c:1009:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜˜˜˜˜
pics.c:1009:9: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^˜˜˜˜˜
pics.c:1000:15: warning: unused variable ‘k’ [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function ‘BIC’:
pics.c:1272:96: warning: unused variable ‘k’ [-Wunused-variable]
int nu=INTEGER(nuC)[0], K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R), i=0, j=0, k=0, N, type=INTEGER(mselect)[0];
^
pics.c: In function ‘getInfMat’:
pics.c:1633:76: warning: unused variable ‘PhiRw’ [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^˜˜˜˜
pics.c:1633:69: warning: unused variable ‘PhiFw’ [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^˜˜˜˜
pics.c: In function ‘mergePeak’:
pics.c:1889:11: warning: unused variable ‘j’ [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c: In function ‘BIC’:
pics.c:1307:6: warning: ‘penalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pics.c: In function ‘fitModelK’:
pics.c:421:18: warning: ‘firstFit’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans, temp, firstFit;
^˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:123:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(length(contF)>0 & length(contR)>0)
segment.c:114:45: warning: unused variable ‘count’ [-Wunused-variable]
int i=0,nR=length(dataR),nF=length(dataF),count=0,lengthCenter=0;
^˜˜˜˜
segment.c: In function ‘callRegions’:
segment.c:308:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0,p=0;
^
segment.c: In function ‘getSegL’:
segment.c:1364:11: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, n=length(list), nF, nR, nProtect=0;
^
segment.c: In function ‘getDensity’:
segment.c:1543:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if((delta[k]>deltaFilter[0] & delta[k]<deltaFilter[1]) &
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
segment.c:1544:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(sF[k]>sFFilter[0] & sF[k]<sFFilter[1]) &
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
segment.c:1545:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(sR[k]>sRFilter[0] & sR[k]<sRFilter[1]) &
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
segment.c:1546:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(se[k]>seFilter[0] & se[k]<seFilter[1]) &
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
segment.c:1547:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(se[k]>seFilterF[0] & se[k]<seFilterF[1]) &
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
segment.c:1548:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(se[k]>seFilterR[0] & se[k]<seFilterR[1]) &
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
segment.c:1549:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
(score[k]>scoreFilter[0] & score[k]<scoreFilter[1]))
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
segment.c:1494:19: warning: variable ‘chr’ set but not used [-Wunused-but-set-variable]
SEXP ans, x, y, chr, names;
^˜˜
segment.c:1490:8: warning: unused variable ‘filter1’ [-Wunused-variable]
SEXP filter1;
^˜˜˜˜˜˜
segment.c:1489:11: warning: unused variable ‘muFilter’ [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^˜˜˜˜˜˜˜
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o PICS.so pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-PICS/00new/PICS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PICS)
