* installing *source* package 'Rtwobitlib' ... ** package 'Rtwobitlib' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' make[1]: Entering directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src' cd "kent" && make -f "Makefile.Rtwobitlib.win" make[2]: Entering directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src/kent' gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 common.c -o common.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 localmem.c -o localmem.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 errAbort.c -o errAbort.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 hash.c -o hash.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 bits.c -o bits.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 cheapcgi.c -o cheapcgi.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 linefile.c -o linefile.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 obscure.c -o obscure.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 dnautil.c -o dnautil.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 dnaseq.c -o dnaseq.o gcc -c -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -ID:/RCompile/recent/R-4.3.3/include -D_FILE_OFFSET_BITS=64 twoBit.c -o twoBit.o ar -rc libtwobit.a common.o localmem.o errAbort.o hash.o bits.o cheapcgi.o linefile.o obscure.o dnautil.o dnaseq.o twoBit.o ranlib libtwobit.a ## We will need -lcrypto only if we decide to support the ## twoBitOpenExternalBptIndex functionality. See NOTES.txt in this ## folder and Rtwobitlib/inst/unused_but_kept_just_in_case/README.txt ## for more information. #gcc -shared -LD:/RCompile/recent/R-4.3.3/bin/x64 -o libtwobit.so common.o localmem.o errAbort.o hash.o bits.o cheapcgi.o linefile.o obscure.o dnautil.o dnaseq.o twoBit.o -lcrypto -lR gcc -shared -LD:/RCompile/recent/R-4.3.3/bin/x64 -o libtwobit.so common.o localmem.o errAbort.o hash.o bits.o cheapcgi.o linefile.o obscure.o dnautil.o dnaseq.o twoBit.o -lR make[2]: Leaving directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src/kent' mkdir -p "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" cd "kent" && cp *.h "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobit_roundtrip.c -o twobit_roundtrip.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobit_seqstats.c -o twobit_seqstats.o mkdir -p "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/x64" cd "kent" && cp libtwobit.a "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/x64" gcc -shared -s -static-libgcc -o Rtwobitlib.dll tmp.def R_init_Rtwobitlib.o Rtwobitlib_utils.o twobit_roundtrip.o twobit_seqstats.o d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/x64/libtwobit.a -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR make[1]: Leaving directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src' make[1]: Entering directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src' cd "kent" && make -f "Makefile.Rtwobitlib.win" make[2]: Entering directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src/kent' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src/kent' mkdir -p "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" cd "kent" && cp *.h "d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobit_roundtrip.c -o twobit_roundtrip.o gcc -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobit_seqstats.c -o twobit_seqstats.o make[1]: Leaving directory '/d/temp/2024_11_15_01_50_00_7107/Rtmp4qN9Y7/R.INSTALL538c3972b70/Rtwobitlib/src' installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-Rtwobitlib/00new/Rtwobitlib/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * MD5 sums packaged installation of 'Rtwobitlib' as Rtwobitlib_0.3.6.zip * DONE (Rtwobitlib)