This page was generated on 2018-04-12 13:21:36 -0400 (Thu, 12 Apr 2018).
install for i386
* installing *source* package 'PING' ...
**********************************************
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˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
^
ping.c: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
^
ping.c: In function 'ECM1':
ping.c:912:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1072:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:760:15: 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);
^
ping.c: In function 'ECM1PE':
ping.c:1320:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1473:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1527:15: 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);
^
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR;
^
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
double tstat=0.0,tstatMax=0.0;
^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c: In function 'BIC':
ping.c:2101:6: 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;
^
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
^
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans, temp, firstFit;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.buildbin-libdir/PING/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'PING'
finding HTML links ... done
CoverageTrack html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/CoverageTrack.Rd:32: missing file link 'AnnotationTrack'
NucleosomeTrack html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:21: missing file link 'AnnotationTrack'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:34: missing file link 'DataTrack'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/NucleosomeTrack.Rd:35: missing file link 'AnnotationTrack'
PICS_IMPORT html
PING html
RawReadsTrack html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcj0Koc/R.INSTALL34406fe84bc5/PING/man/RawReadsTrack.Rd:33: missing file link 'DataTrack'
ping-class html
pingError-class html
pingList-class html
plotSummary html
postPING html
segmentPING html
show html
summary html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'PING' ...
**********************************************
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˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
^
ping.c: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
^
ping.c: In function 'ECM1':
ping.c:912:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1072:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:760:15: 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);
^
ping.c: In function 'ECM1PE':
ping.c:1320:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1473:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1527:15: 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);
^
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR;
^
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
double tstat=0.0,tstatMax=0.0;
^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c: In function 'BIC':
ping.c:2101:6: 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;
^
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
^
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans, temp, firstFit;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/PING.buildbin-libdir/PING/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PING' as PING_2.22.0.zip
* DONE (PING)
In R CMD INSTALL
In R CMD INSTALL