* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* 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: ‘Debian clang version 21.1.6 (2)’
using Fortran compiler: ‘Debian flang version 21.1.6 (2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkg3dk7/R.INSTALL3d6e8c1d6fbf6e/bqtl/src'
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c bc1wt.c -o bc1wt.o
In file included from bc1wt.c:7:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c conCk.c -o conCk.o
In file included from conCk.c:5:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c condreg.c -o condreg.o
In file included from condreg.c:28:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c f2wt2.c -o f2wt2.o
In file included from f2wt2.c:7:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
flang-21  -fpic  -g -O2 -c hessup.f -o hessup.o
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c hkreg.c -o hkreg.o
In file included from hkreg.c:6:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c lapWHL.c -o lapWHL.o
In file included from lapWHL.c:7:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c lapadj.c -o lapadj.o
In file included from lapadj.c:13:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c llkEm.c -o llkEm.o
In file included from llkEm.c:7:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c normLogLik.c -o normLogLik.o
In file included from normLogLik.c:6:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c swapbc1.c -o swapbc1.o
In file included from swapbc1.c:41:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c swapf2.c -o swapf2.o
In file included from swapf2.c:40:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twohkbc1.c -o twohkbc1.o
In file included from twohkbc1.c:13:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c twohkf2.c -o twohkf2.o
In file included from twohkf2.c:15:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c upbqtl.c -o upbqtl.o
In file included from upbqtl.c:14:
In file included from ./lapadj.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^
1 warning generated.
clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkg3dk7/R.INSTALL3d6e8c1d6fbf6e/bqtl/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkg3dk7/R.INSTALL3d6e8c1d6fbf6e/bqtl/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkg3dk7/R.INSTALL3d6e8c1d6fbf6e/bqtl/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)