############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PICS_2.38.0.tar.gz && rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PICS.buildbin-libdir PICS_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PICS_2.38.0.zip && rm PICS_2.38.0.tar.gz PICS_2.38.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 67 658k 67 444k 0 0 842k 0 --:--:-- --:--:-- --:--:-- 842k 100 658k 100 658k 0 0 972k 0 --:--:-- --:--:-- --:--:-- 971k install for i386 * installing *source* package 'PICS' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pics.c -o pics.o pics.c: In function 'ECM2': pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum, etaF, etaR, dd, cc; ^~~~~~ 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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c segment.c -o segment.o segment.c: In function 'getDensity': 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:/rtools40/mingw32/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-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-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 bam2gr html candidate.region html makeGRangesOutput html pics-class html pics-generics html picsError-class html picsFDR html picsList-class html plot-FDR html plot-pics html segChrRead html segReads-class html segReadsGeneric html segReadsListPE-class html segReadsPE-class html segmentPICS html setParaEM html setParaPrior 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pics.c -o pics.o pics.c: In function 'ECM2': pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum, etaF, etaR, dd, cc; ^~~~~~ 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c segment.c -o segment.o segment.c: In function 'getDensity': 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:/rtools40/mingw64/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-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/PICS.buildbin-libdir/PICS/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'PICS' as PICS_2.38.0.zip * DONE (PICS) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'PICS' successfully unpacked and MD5 sums checked