* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘Rtwobitlib’ ...
** this is package ‘Rtwobitlib’ version ‘0.3.6’
** package ‘Rtwobitlib’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 19.1.7 (1+b1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src'
cd "kent" && make -f "Makefile.Rtwobitlib"
make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src/kent'
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 common.c -o common.o
In file included from common.c:7:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 localmem.c -o localmem.o
In file included from localmem.c:11:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 errAbort.c -o errAbort.o
In file included from errAbort.c:25:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 hash.c -o hash.o
In file included from hash.c:6:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 bits.c -o bits.o
In file included from bits.c:6:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 cheapcgi.c -o cheapcgi.o
In file included from cheapcgi.c:7:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 linefile.c -o linefile.o
In file included from linefile.c:7:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 obscure.c -o obscure.o
In file included from obscure.c:6:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 dnautil.c -o dnautil.o
In file included from dnautil.c:15:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 dnaseq.c -o dnaseq.o
In file included from dnaseq.c:6:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -c -g -O3 -Wall -pedantic -fpic -I/usr/local/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -D_FILE_OFFSET_BITS=64 twoBit.c -o twoBit.o
In file included from twoBit.c:4:
./common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
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.
#clang-19 -std=gnu23 -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
clang-19 -std=gnu23 -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/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src/kent'
mkdir -p "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
cd "kent" && cp *.h "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o
In file included from Rtwobitlib_utils.c:1:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twobit_roundtrip.c -o twobit_roundtrip.o
In file included from twobit_roundtrip.c:2:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twobit_seqstats.c -o twobit_seqstats.o
In file included from twobit_seqstats.c:2:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
mkdir -p "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib"
cd "kent" && cp libtwobit.so libtwobit.a "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib"
cd "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib" && ln -s libtwobit.so libtwobit.so.2
clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/usrlib/libtwobit.a -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src'
cd "kent" && make -f "Makefile.Rtwobitlib"
make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src/kent'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src/kent'
mkdir -p "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
cd "kent" && cp *.h "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent"
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Rtwobitlib.c -o R_init_Rtwobitlib.o
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Rtwobitlib_utils.c -o Rtwobitlib_utils.o
In file included from Rtwobitlib_utils.c:1:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twobit_roundtrip.c -o twobit_roundtrip.o
In file included from twobit_roundtrip.c:2:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
clang-19 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twobit_seqstats.c -o twobit_seqstats.o
In file included from twobit_seqstats.c:2:
In file included from ./Rtwobitlib_utils.h:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/twoBit.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:90:9: warning: keyword is hidden by macro definition [-Wkeyword-macro]
   90 | #define bool char
      |         ^
1 warning generated.
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6JGHmU/R.INSTALL266d9661a11699/Rtwobitlib/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/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)