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### Running command:
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### 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
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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
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
