* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘qtl’ ...
** this is package ‘qtl’ version ‘1.72’
** package ‘qtl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-9) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
make[1]: Entering directory '/tmp/RtmpPkNZ6w/R.INSTALL221783713af1f9/qtl/src'
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init.c -o R_init.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c countXO.c -o countXO.o
In file included from countXO.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c discan.c -o discan.o
In file included from discan.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c discan_covar.c -o discan_covar.o
In file included from discan_covar.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c effectscan.c -o effectscan.o
In file included from effectscan.c:38:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fill_geno_nodblXO.c -o fill_geno_nodblXO.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c findDupMarkers_notexact.c -o findDupMarkers_notexact.o
In file included from findDupMarkers_notexact.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitqtl_hk.c -o fitqtl_hk.o
In file included from fitqtl_hk.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitqtl_hk_binary.c -o fitqtl_hk_binary.o
In file included from fitqtl_hk_binary.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitqtl_imp.c -o fitqtl_imp.o
In file included from fitqtl_imp.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitqtl_imp_binary.c -o fitqtl_imp_binary.o
In file included from fitqtl_imp_binary.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c forwsel.c -o forwsel.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_4way.c -o hmm_4way.o
In file included from hmm_4way.c:45:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_bc.c -o hmm_bc.o
In file included from hmm_bc.c:43:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_bci.c -o hmm_bci.o
In file included from hmm_bci.c:50:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_bcsft.c -o hmm_bcsft.o
In file included from hmm_bcsft.c:43:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_bgmagic16.c -o hmm_bgmagic16.o
In file included from hmm_bgmagic16.c:45:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_f2.c -o hmm_f2.o
In file included from hmm_f2.c:42:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_f2i.c -o hmm_f2i.o
In file included from hmm_f2i.c:49:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_main.c -o hmm_main.o
In file included from hmm_main.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_ri4self.c -o hmm_ri4self.o
In file included from hmm_ri4self.c:45:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_ri4sib.c -o hmm_ri4sib.o
In file included from hmm_ri4sib.c:45:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_ri8self.c -o hmm_ri8self.o
In file included from hmm_ri8self.c:45:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_ri8selfIRIP1.c -o hmm_ri8selfIRIP1.o
In file included from hmm_ri8selfIRIP1.c:44:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_ri8sib.c -o hmm_ri8sib.o
In file included from hmm_ri8sib.c:46:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmm_util.c -o hmm_util.o
In file included from hmm_util.c:34:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c inferFounderHap.c -o inferFounderHap.o
In file included from inferFounderHap.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c info.c -o info.o
In file included from info.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lapackutil.c -o lapackutil.o
In file included from lapackutil.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c markerlrt.c -o markerlrt.o
In file included from markerlrt.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmaugment.cpp -o mqmaugment.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmdatatypes.cpp -o mqmdatatypes.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmeliminate.cpp -o mqmeliminate.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmmapqtl.cpp -o mqmmapqtl.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmmixture.cpp -o mqmmixture.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmprob.cpp -o mqmprob.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmregression.cpp -o mqmregression.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mqmscan.cpp -o mqmscan.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pickMarkerSubset.c -o pickMarkerSubset.o
In file included from pickMarkerSubset.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ril48_reorg.c -o ril48_reorg.o
In file included from ril48_reorg.c:38:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ripple.c -o ripple.o
In file included from ripple.c:38:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_ehk.c -o scanone_ehk.o
In file included from scanone_ehk.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_em.c -o scanone_em.o
In file included from scanone_em.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_em_covar.c -o scanone_em_covar.o
In file included from scanone_em_covar.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_hk.c -o scanone_hk.o
In file included from scanone_hk.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_hk_binary.c -o scanone_hk_binary.o
In file included from scanone_hk_binary.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_imp.c -o scanone_imp.o
In file included from scanone_imp.c:39:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_mr.c -o scanone_mr.o
In file included from scanone_mr.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scanone_np.c -o scanone_np.o
In file included from scanone_np.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_binary_em.c -o scantwo_binary_em.o
In file included from scantwo_binary_em.c:39:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_binary_hk.c -o scantwo_binary_hk.o
In file included from scantwo_binary_hk.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_em.c -o scantwo_em.o
In file included from scantwo_em.c:38:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_hk.c -o scantwo_hk.o
In file included from scantwo_hk.c:37:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_imp.c -o scantwo_imp.o
In file included from scantwo_imp.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwo_mr.c -o scantwo_mr.o
In file included from scantwo_mr.c:38:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scantwopermhk.c -o scantwopermhk.o
In file included from scantwopermhk.c:10:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c simulate.c -o simulate.o
In file included from simulate.c:35:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c simulate_ril.c -o simulate_ril.o
In file included from simulate_ril.c:39:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stahl_mf.c -o stahl_mf.o
In file included from stahl_mf.c:41:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c summary_scantwo.c -o summary_scantwo.o
In file included from summary_scantwo.c:36:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c test_bcsft.c -o test_bcsft.o
In file included from test_bcsft.c:44:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vbscan.c -o vbscan.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zeroin.c -o zeroin.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o qtl.so R_init.o countXO.o discan.o discan_covar.o effectscan.o fill_geno_nodblXO.o findDupMarkers_notexact.o fitqtl_hk.o fitqtl_hk_binary.o fitqtl_imp.o fitqtl_imp_binary.o forwsel.o hmm_4way.o hmm_bc.o hmm_bci.o hmm_bcsft.o hmm_bgmagic16.o hmm_f2.o hmm_f2i.o hmm_main.o hmm_ri4self.o hmm_ri4sib.o hmm_ri8self.o hmm_ri8selfIRIP1.o hmm_ri8sib.o hmm_util.o inferFounderHap.o info.o lapackutil.o markerlrt.o mqmaugment.o mqmdatatypes.o mqmeliminate.o mqmmapqtl.o mqmmixture.o mqmprob.o mqmregression.o mqmscan.o pickMarkerSubset.o ril48_reorg.o ripple.o scanone_ehk.o scanone_em.o scanone_em_covar.o scanone_hk.o scanone_hk_binary.o scanone_imp.o scanone_mr.o scanone_np.o scantwo_binary_em.o scantwo_binary_hk.o scantwo_em.o scantwo_hk.o scantwo_imp.o scantwo_mr.o scantwopermhk.o simulate.o simulate_ril.o stahl_mf.o summary_scantwo.o test_bcsft.o util.o vbscan.o zeroin.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpPkNZ6w/R.INSTALL221783713af1f9/qtl/src'
make[1]: Entering directory '/tmp/RtmpPkNZ6w/R.INSTALL221783713af1f9/qtl/src'
make[1]: Leaving directory '/tmp/RtmpPkNZ6w/R.INSTALL221783713af1f9/qtl/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-qtl/00new/qtl/libs
** R
** data
** 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 (qtl)