* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bqtl’ ...
** package ‘bqtl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpPxQmyX/R.INSTALL1f421f7e20190/bqtl/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bc1wt.c -o bc1wt.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c conCk.c -o conCk.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c condreg.c -o condreg.o
condreg.c: In function ‘resmat’:
condreg.c:70:13: warning: variable ‘one’ set but not used [-Wunused-but-set-variable]
70 | longint one[1];
| ^~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c f2wt2.c -o f2wt2.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c hessup.f -o hessup.o
hessup.f:13:59:
13 | $ reset, bk, newhss, bks, qrbk, paradj, np ,newprm)
| 1
Warning: Unused dummy argument ‘newprm’ at (1) [-Wunused-dummy-argument]
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hkreg.c -o hkreg.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lapWHL.c -o lapWHL.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lapadj.c -o lapadj.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c llkEm.c -o llkEm.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c normLogLik.c -o normLogLik.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c swapbc1.c -o swapbc1.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c swapf2.c -o swapf2.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twohkbc1.c -o twohkbc1.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c twohkf2.c -o twohkf2.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c upbqtl.c -o upbqtl.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpPxQmyX/R.INSTALL1f421f7e20190/bqtl/src'
make[1]: Entering directory '/tmp/RtmpPxQmyX/R.INSTALL1f421f7e20190/bqtl/src'
make[1]: Leaving directory '/tmp/RtmpPxQmyX/R.INSTALL1f421f7e20190/bqtl/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bqtl/00new/bqtl/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bqtl’
finding HTML links ... done
a.starting.point.for.bqtl html
adjust.linear.bayes html
bqtl-internal html
bqtl html
coef.bqtl html
configs html
covar html
formula.bqtl html
lapadj html
linear.bayes html
little.ana.bc html
little.ana.f2 html
little.bc.markers html
little.bc.pheno html
little.dx html
little.f2.markers html
little.f2.pheno html
little.map.frame html
little.mf.5 html
locus html
loglik html
make.analysis.obj html
make.loc.right html
make.location.prior html
make.map.frame html
make.marker.numeric html
make.regressor.matrix html
make.state.matrix html
make.varcov html
map.index html
map.location html
map.names html
marker.fill html
marker.levels html
plot.map.frame html
predict.bqtl html
predict.linear.bayes html
residuals.bqtl html
summary.adj html
summary.bqtl html
summary.map.frame html
summary.swap html
swap html
swapbc1 html
swapf2 html
twohk html
twohkbc1 html
update.bqtl html
varcov html
** 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)