############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cn.mops_1.40.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.40.0.zip && rm cn.mops_1.40.0.tar.gz cn.mops_1.40.0.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 97 630k 97 615k 0 0 1174k 0 --:--:-- --:--:-- --:--:-- 1174k 100 630k 100 630k 0 0 1196k 0 --:--:-- --:--:-- --:--:-- 1196k install for i386 * installing *source* package 'cn.mops' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnmops.c -o R_init_cnmops.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cnmops.cpp -o cnmops.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c segment.cpp -o segment.o segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^~~~~~~~ segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable] double oldStatistic, meanLeft,meanRight,varLeft,varRight; ^~~~~~~~~~~~ segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable] double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1; ^~~~~~~~~~~~ segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable] double newPValue, maxPValue,oldPValue,maxIdx; ^~~~~~ In file included from segment.cpp:10: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: unused variable 'Rf_beta' [-Wunused-variable] #define beta Rf_beta ^~~~~~~ segment.cpp:64:9: note: in expansion of macro 'beta' double beta,nn; ^~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -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/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cn.mops' finding HTML links ... done CNVDetectionResult html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/cnvdetectionresult.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/CnvDetectionResult.html CNVRanges html X html XRanges html calcFractionalCopyNumbers-CNVDetectionResult-method html calcFractionalCopyNumbers html calcIntegerCopyNumbers-CNVDetectionResult-method html calcIntegerCopyNumbers html cn.mops html cnvr-CNVDetectionResult-method html cnvr html cnvs-CNVDetectionResult-method html cnvs html exomeCounts html exomecn.mops html getReadCountsFromBAM html getSegmentReadCountsFromBAM html gr-CNVDetectionResult-method html gr html haplocn.mops html individualCall-CNVDetectionResult-method html individualCall html iniCall-CNVDetectionResult-method html iniCall html integerCopyNumber-CNVDetectionResult-method html integerCopyNumber html localAssessments-CNVDetectionResult-method html localAssessments html makeRobustCNVR html normalizeChromosomes html normalizeGenome html normalizedData-CNVDetectionResult-method html normalizedData html params-CNVDetectionResult-method html params html plot html posteriorProbs-CNVDetectionResult-method html posteriorProbs html referencecn.mops html sampleNames-CNVDetectionResult-method html sampleNames html segment html segmentation-CNVDetectionResult-method html segmentation html segplot-CNVDetectionResult-method html segplot html show html singlecn.mops 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 'cn.mops' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnmops.c -o R_init_cnmops.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cnmops.cpp -o cnmops.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c segment.cpp -o segment.o segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^~~~~~~~ segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable] double oldStatistic, meanLeft,meanRight,varLeft,varRight; ^~~~~~~~~~~~ segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable] double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1; ^~~~~~~~~~~~ segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable] double newPValue, maxPValue,oldPValue,maxIdx; ^~~~~~ In file included from segment.cpp:10: C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: unused variable 'Rf_beta' [-Wunused-variable] #define beta Rf_beta ^~~~~~~ segment.cpp:64:9: note: in expansion of macro 'beta' double beta,nn; ^~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -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/cn.mops.buildbin-libdir/cn.mops/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'cn.mops' as cn.mops_1.40.0.zip * DONE (cn.mops) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'cn.mops' successfully unpacked and MD5 sums checked