* installing *source* package ‘bqtl’ ...
** this is package ‘bqtl’ version ‘1.0-38’
** package ‘bqtl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.6’
using Fortran compiler: ‘flang version 21.1.6’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bqtl/src'
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c bc1wt.c -o bc1wt.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c conCk.c -o conCk.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c condreg.c -o condreg.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c f2wt2.c -o f2wt2.o
In file included from bc1wt.c:7:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from conCk.c:5:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
/usr/local/clang21/bin/flang  -fpic  -O2 -pedantic  -c hessup.f -o hessup.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hkreg.c -o hkreg.o
In file included from condreg.c:28:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from f2wt2.c:7:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c init.c -o init.o
In file included from hkreg.c:6:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c lapWHL.c -o lapWHL.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c lapadj.c -o lapadj.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c llkEm.c -o llkEm.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c normLogLik.c -o normLogLik.o
In file included from lapadj.c:13:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from lapWHL.c:7:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from llkEm.c:7:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c swapbc1.c -o swapbc1.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c swapf2.c -o swapf2.o
In file included from normLogLik.c:6:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c twohkbc1.c -o twohkbc1.o
In file included from swapbc1.c:41:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from swapf2.c:40:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from twohkbc1.c:13:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c twohkf2.c -o twohkf2.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c upbqtl.c -o upbqtl.o
1 warning generated.
In file included from twohkf2.c:15:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
In file included from upbqtl.c:14:
In file included from ./lapadj.h:8:
/data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   31 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o bqtl.so bc1wt.o conCk.o condreg.o f2wt2.o hessup.o hkreg.o init.o lapWHL.o lapadj.o llkEm.o normLogLik.o swapbc1.o swapf2.o twohkbc1.o twohkf2.o upbqtl.o -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bqtl/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bqtl/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bqtl/src'
installing to /data/gannet/ripley/R/packages/tests-clang/bqtl.Rcheck/00LOCK-bqtl/00new/bqtl/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (bqtl)