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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PICS_2.27.0.tar.gz && rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PICS.buildbin-libdir PICS_2.27.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PICS_2.27.0.zip && rm PICS_2.27.0.tar.gz PICS_2.27.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 813k 100 813k 0 0 12.4M 0 --:--:-- --:--:-- --:--:-- 14.4M
install for i386
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/PICS.buildbin-libdir/00LOCK-PICS/00new/PICS/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PICS'
finding HTML links ... done
PICS html
SegReadsList html
bam2gr html
makeRangedDataOutput html
pics-class html
picsError-class html
picsFDR html
picsList-class html
plot-FDR html
segChrRead html
segReads html
segReadsListPE html
segReadsPE html
segmentPICS html
setParaEM html
setParaPrior html
show html
summary html
summarySeg html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PICS' as PICS_2.27.0.zip
* DONE (PICS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PICS' successfully unpacked and MD5 sums checked
