############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/inveRsion_1.40.0.tar.gz && rm -rf inveRsion.buildbin-libdir && mkdir inveRsion.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=inveRsion.buildbin-libdir inveRsion_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL inveRsion_1.40.0.zip && rm inveRsion_1.40.0.tar.gz inveRsion_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 0 451k 0 3837 0 0 4294 0 0:01:47 --:--:-- 0:01:47 4296 100 451k 100 451k 0 0 388k 0 0:00:01 0:00:01 --:--:-- 388k install for i386 * installing *source* package 'inveRsion' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_inveRsion.c -o init_inveRsion.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inversionModel.c -o inversionModel.o inversionModel.c: In function 'blockAndLev': inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level]) ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ inversionModel.c: In function 'inversionModel': inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] while(steps<*maxSteps & tol>mintol) ~~~~~^~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writeGenoDat.c -o writeGenoDat.o writeGenoDat.c: In function 'writeGenoDat': writeGenoDat.c:34:16: warning: 'dat' may be used uninitialized in this function [-Wmaybe-uninitialized] int i,j,l,k,dat,nomiss[*numlevcaco],sum[*numlevcaco]; ^~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o inveRsion.dll tmp.def init_inveRsion.o inversionModel.o writeGenoDat.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/inveRsion.buildbin-libdir/00LOCK-inveRsion/00new/inveRsion/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'inveRsion' finding HTML links ... done GenoDat-class html GenoDatROI-class html HaploCode-class html ac html accBic html accuracy-class html codeHaplo html gDat html getClassif-methods html getInv-methods html getROIs-methods html hapCode html invList html inveRsion-internal html inveRsion-package html inversion-class html inversionList-class html listInv-methods html scan-class html scanInv html scanRes html setUpGenoDatFile 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 'inveRsion' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_inveRsion.c -o init_inveRsion.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inversionModel.c -o inversionModel.o inversionModel.c: In function 'blockAndLev': inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level]) ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ inversionModel.c: In function 'inversionModel': inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] while(steps<*maxSteps & tol>mintol) ~~~~~^~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writeGenoDat.c -o writeGenoDat.o writeGenoDat.c: In function 'writeGenoDat': writeGenoDat.c:34:16: warning: 'dat' may be used uninitialized in this function [-Wmaybe-uninitialized] int i,j,l,k,dat,nomiss[*numlevcaco],sum[*numlevcaco]; ^~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o inveRsion.dll tmp.def init_inveRsion.o inversionModel.o writeGenoDat.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/inveRsion.buildbin-libdir/inveRsion/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'inveRsion' as inveRsion_1.40.0.zip * DONE (inveRsion) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'inveRsion' successfully unpacked and MD5 sums checked