Install log for 'nonmem2rx'

* installing *source* package ‘nonmem2rx’ ...
** package ‘nonmem2rx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.4’
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/nonmem2rx/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c abbrec.c -o abbrec.o
In file included from abbrec.c:21:
./abbrec.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c abbrev.c -o abbrev.o
In file included from abbrev.c:21:
./abbrev.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c data.c -o data.o
In file included from data.c:21:
./data.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c init.c -o init.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c input.c -o input.o
In file included from input.c:21:
./input.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c lst.c -o lst.o
In file included from lst.c:21:
./lst.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c mem.c -o mem.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c model.c -o model.o
In file included from model.c:21:
./model.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nonmemId.cpp -o nonmemId.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c omega.c -o omega.o
In file included from omega.c:21:
./omega.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c records.c -o records.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c sbuf.c -o sbuf.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c strncmpi.c -o strncmpi.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c sub.c -o sub.o
In file included from sub.c:21:
./sub.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c tab.c -o tab.o
In file included from tab.c:21:
./tab.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c theta.c -o theta.o
In file included from theta.c:21:
./theta.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
    3 | #define printf Rprintf
      |         ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
   89 | #  define printf(...) \
      |           ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c util.cpp -o util.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/dparser/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c validate.c -o validate.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o nonmem2rx.so RcppExports.o abbrec.o abbrev.o data.o init.o input.o lst.o mem.o model.o nonmemId.o omega.o records.o sbuf.o strncmpi.o sub.o tab.o theta.o util.o validate.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/nonmem2rx/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/nonmem2rx/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/nonmem2rx/src'
installing to /data/gannet/ripley/R/packages/tests-clang/nonmem2rx.Rcheck/00LOCK-nonmem2rx/00new/nonmem2rx/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 (nonmem2rx)