Install log for 'Rtwobitlib'

* installing *source* package ‘Rtwobitlib’ ...
** package ‘Rtwobitlib’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.0.1 20240503 (prerelease)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src'
cd "kent" && make -f "Makefile.Rtwobitlib"
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src/kent'
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 common.c -o common.o
mkdir -p "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
mkdir -p "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib"
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 localmem.c -o localmem.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 errAbort.c -o errAbort.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 hash.c -o hash.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 bits.c -o bits.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 cheapcgi.c -o cheapcgi.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 linefile.c -o linefile.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 obscure.c -o obscure.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 dnautil.c -o dnautil.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 dnaseq.c -o dnaseq.o
gcc-14 -c -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -I/usr/local/include -I/data/gannet/ripley/R/R-devel/include -D_FILE_OFFSET_BITS=64 twoBit.c -o twoBit.o
gcc-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
gcc-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 -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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 -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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 '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src/kent'
cd "kent" && cp *.h "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
cd "kent" && cp libtwobit.so libtwobit.a "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib"
cd "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib" && ln -s libtwobit.so libtwobit.so.2
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c twobit_roundtrip.c -o twobit_roundtrip.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c twobit_seqstats.c -o twobit_seqstats.o
gcc-14 -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o Rtwobitlib.so R_init_Rtwobitlib.o Rtwobitlib_utils.o twobit_roundtrip.o twobit_seqstats.o /data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/libtwobit.a
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src'
cd "kent" && make -f "Makefile.Rtwobitlib"
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src/kent'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src/kent'
mkdir -p "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
cd "kent" && cp *.h "/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c twobit_roundtrip.c -o twobit_roundtrip.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c twobit_seqstats.c -o twobit_seqstats.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Rtwobitlib/src'
installing to /data/gannet/ripley/R/packages/tests-devel/Rtwobitlib.Rcheck/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)