* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’ * installing *source* package ‘Rtwobitlib’ ... ** package ‘Rtwobitlib’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src' cd "kent" && make -f "Makefile.Rtwobitlib" make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src/kent' gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 common.c -o common.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 localmem.c -o localmem.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 errAbort.c -o errAbort.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 hash.c -o hash.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 bits.c -o bits.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 cheapcgi.c -o cheapcgi.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 linefile.c -o linefile.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 obscure.c -o obscure.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 dnautil.c -o dnautil.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/include -D_FILE_OFFSET_BITS=64 dnaseq.c -o dnaseq.o gcc-14 -c -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-release-gcc/Work/build/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-14 -shared -Wl,-O1 -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 gcc-14 -shared -Wl,-O1 -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 make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src/kent' mkdir -p "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" cd "kent" && cp *.h "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twobit_roundtrip.c -o twobit_roundtrip.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twobit_seqstats.c -o twobit_seqstats.o mkdir -p "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib" cd "kent" && cp libtwobit.so libtwobit.a "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib" cd "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib" && ln -s libtwobit.so libtwobit.so.2 gcc-14 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o Rtwobitlib.so R_init_Rtwobitlib.o Rtwobitlib_utils.o twobit_roundtrip.o twobit_seqstats.o /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/libtwobit.a -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src' cd "kent" && make -f "Makefile.Rtwobitlib" make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src/kent' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src/kent' mkdir -p "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" cd "kent" && cp *.h "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent" gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twobit_roundtrip.c -o twobit_roundtrip.o gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include" -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twobit_seqstats.c -o twobit_seqstats.o make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRZuR23/R.INSTALL1fac895384b3b6/Rtwobitlib/src' installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rtwobitlib)