Install log for 'gap'

* installing *source* package ‘gap’ ...
** this is package ‘gap’ version ‘1.14’
** package ‘gap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 22.1.0 (https://github.com/llvm/llvm-project 4434dabb69916856b824f68a64b029c67175e532)’
using Fortran compiler: ‘flang version 22.1.0 (https://github.com/llvm/llvm-project 4434dabb69916856b824f68a64b029c67175e532)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/gap/src'
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c 2k.c -o 2k.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c 2ld.c -o 2ld.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c cline.c -o cline.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c gcontrol_c.c -o gcontrol_c.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c gcx.c -o gcx.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c gif_c.c -o gif_c.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hap_c.c -o hap_c.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hwe.hardy.c -o hwe.hardy.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c kin.morgan.c -o kin.morgan.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c makeped_c.c -o makeped_c.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c mia.c -o mia.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c muvar.c -o muvar.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c package_native_routine_registration_skeleton.c -o package_native_routine_registration_skeleton.o
flang-22  -fpic  -O2 -pedantic  -c pfc.f -o pfc.o
./pfc.f:12:24: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision zero,const,p,stat(20)
                         ^^^^
./pfc.f:13:15: warning: Value of uninitialized local variable 'maxfac' is used but never defined [-Wused-undefined-variable]
        integer maxfac,m(20),sib,aff,freq,oldsib,ns,
                ^^^^^^
./pfc.f:82:17: warning: Value of uninitialized local variable 'nssave' is used but never defined [-Wused-undefined-variable]
       & ia,ib,ic,nssave
                  ^^^^^^
./pfc.f:83:33: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision stat(20),zero,one,two,dexp,dlog,be,
                                  ^^^^
./pfc.f:83:38: warning: Value of uninitialized local variable 'one' is used but never defined [-Wused-undefined-variable]
        double precision stat(20),zero,one,two,dexp,dlog,be,
                                       ^^^
./pfc.f:83:42: warning: Value of uninitialized local variable 'two' is used but never defined [-Wused-undefined-variable]
        double precision stat(20),zero,one,two,dexp,dlog,be,
                                           ^^^
./pfc.f:84:34: warning: Value of uninitialized local variable 'eps' is used but never defined [-Wused-undefined-variable]
       & binp,sbe,he,she,fmij,dble,eps,chi1,chi2,dsqrt
                                   ^^^
./pfc.f:167:17: warning: Value of uninitialized local variable 'one' is used but never defined [-Wused-undefined-variable]
       &  psum,p0,one,zero,dcase,pasum,proba
                  ^^^
./pfc.f:167:21: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
       &  psum,p0,one,zero,dcase,pasum,proba
                      ^^^^
./pfc.f:169:24: warning: Value of uninitialized local variable 'per' is used but never defined [-Wused-undefined-variable]
       &  nfam,alloc(20),per,mod,ncase
                         ^^^
./pfc.f:248:30: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision const,zero
                               ^^^^
./pfc.f:281:24: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision zero,const,p,dexp,lminf,slf
                         ^^^^
./pfc.f:281:42: warning: Value of uninitialized local variable 'lminf' is used but never defined [-Wused-undefined-variable]
        double precision zero,const,p,dexp,lminf,slf
                                           ^^^^^
./pfc.f:444:35: warning: Value of uninitialized local variable 'lminf' is used but never defined [-Wused-undefined-variable]
        double precision proba,dexp,lminf
                                    ^^^^^
flang-22  -fpic  -O2 -pedantic  -c pfc.sim.f -o pfc.sim.o
./pfc.sim.f:13:24: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision zero,const,obsp,slf,p
                         ^^^^
./pfc.sim.f:15:15: warning: Value of uninitialized local variable 'maxfac' is used but never defined [-Wused-undefined-variable]
        integer maxfac,m(20),sib,aff,freq,oldsib,i,
                ^^^^^^
./pfc.sim.f:205:30: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision const,zero
                               ^^^^
./pfc.sim.f:287:28: warning: Value of uninitialized local variable 'zero' is used but never defined [-Wused-undefined-variable]
        double precision slf,zero,const,p,dexp,lminf
                             ^^^^
./pfc.sim.f:287:46: warning: Value of uninitialized local variable 'lminf' is used but never defined [-Wused-undefined-variable]
        double precision slf,zero,const,p,dexp,lminf
                                               ^^^^^
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c pgc_c.c -o pgc_c.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c whscore.c -o whscore.o
clang-22 -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/22/lib/x86_64-unknown-linux-gnu -o gap.so 2k.o 2ld.o cline.o gcontrol_c.o gcx.o gif_c.o hap_c.o hwe.hardy.o kin.morgan.o makeped_c.o mia.o muvar.o package_native_routine_registration_skeleton.o pfc.o pfc.sim.o pgc_c.o whscore.o -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/gap/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/gap/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/gap/src'
installing to /data/gannet/ripley/R/packages/tests-clang/gap.Rcheck/00LOCK-gap/00new/gap/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
Warning in eval(exprs[i], envir) :
  hwe.cc needs package `MASS' to be fully functional; please install
** 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 (gap)