############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/VanillaICE_1.56.3.tar.gz && rm -rf VanillaICE.buildbin-libdir && mkdir VanillaICE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VanillaICE.buildbin-libdir VanillaICE_1.56.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL VanillaICE_1.56.3.zip && rm VanillaICE_1.56.3.tar.gz VanillaICE_1.56.3.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 9 1100k 9 101k 0 0 535k 0 0:00:02 --:--:-- 0:00:02 536k 100 1100k 100 1100k 0 0 1228k 0 --:--:-- --:--:-- --:--:-- 1228k install for i386 * installing *source* package 'VanillaICE' ... ** 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 rinit.c -o rinit.o "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 viterbi.c -o viterbi.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -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/VanillaICE.buildbin-libdir/00LOCK-VanillaICE/00new/VanillaICE/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Creating a new generic function for 'distance' in package 'VanillaICE' ** help *** installing help indices converting help for package 'VanillaICE' finding HTML links ... done ArrayViews-class html CopyNumScanParams html finding level-2 HTML links ... done EmissionParam-methods html FilterParam-class html HMM html HMMList-class html HMMList html HmmGRanges-methods html HmmParam html HmmTrellisParam html IO html IdiogramParam-class html IdiogramParams-class html LogLik-class html LogLik html LowLevelSummaries html NA_filter html SnpArrayExperiment-class html SnpExperiment html SnpGRanges html TransitionParam html VanillaICE html Viterbi-methods html acf2 html baumWelchUpdate html calculateEmission html cnvFilter html doUpdate html dropDuplicatedMapLocs html dropSexChrom html emission html emissionParam html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.buildbin-libdir/00LOCK-VanillaICE/00new/VanillaICE/help/emissionParam.html filters html getExampleSnpExperiment html getHmmParams html hmm2 html hmmResults html isHeterozygous html matrixOrNULL-class html numberFeatures html parseSourceFile html parsedPath html plotting html probability html rescale html robust-statistics html segs html snpArrayAssays html snp_exp html sourcePaths html start-oligoSnpSet-method html state-methods html sweepMode html threshold html updateHmmParams html viewports html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package can be loaded from final location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'VanillaICE' ... ** 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 rinit.c -o rinit.o "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 viterbi.c -o viterbi.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -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/VanillaICE.buildbin-libdir/VanillaICE/libs/x64 ** testing if installed package can be loaded No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' * MD5 sums packaged installation of 'VanillaICE' as VanillaICE_1.56.3.zip * DONE (VanillaICE) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'VanillaICE' successfully unpacked and MD5 sums checked