* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘gap’ ...
** package ‘gap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-24) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/Rtmphvi55G/R.INSTALL32e62a39551e5b/gap/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 2k.c -o 2k.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 2ld.c -o 2ld.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 cline.c -o cline.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 gcontrol_c.c -o gcontrol_c.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 gcx.c -o gcx.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 gif_c.c -o gif_c.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 hap_c.c -o hap_c.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 hwe.hardy.c -o hwe.hardy.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 kin.morgan.c -o kin.morgan.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 makeped_c.c -o makeped_c.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 mia.c -o mia.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 muvar.c -o muvar.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 package_native_routine_registration_skeleton.c -o package_native_routine_registration_skeleton.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c pfc.f -o pfc.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c pfc.sim.f -o pfc.sim.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 pgc_c.c -o pgc_c.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 whscore.c -o whscore.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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 -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmphvi55G/R.INSTALL32e62a39551e5b/gap/src'
make[1]: Entering directory '/tmp/Rtmphvi55G/R.INSTALL32e62a39551e5b/gap/src'
make[1]: Leaving directory '/tmp/Rtmphvi55G/R.INSTALL32e62a39551e5b/gap/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-gap/00new/gap/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘gap’
finding HTML links ... done
AE3 html
BFDP html
ESplot html
FPRP html
KCC html
LD22 html
LDkl html
MCMCgrm html
METAL_forestplot html
ReadGRM html
ReadGRMBin html
SNP html
WriteGRM html
WriteGRMBin html
a2g html
ab html
allele.recode html
asplot html
b2r html
bt html
ccsize html
chow.test html
chr_pos_a1_a2 html
ci2ms html
circos.cis.vs.trans.plot html
circos.cnvplot html
circos.mhtplot html
circos.mhtplot2 html
cis.vs.trans.classification html
cnvplot html
comp.score html
cs html
fbsize html
g2a html
gap html
gc.em html
gc.lambda html
gcontrol html
gcontrol2 html
gcp html
genecounting html
geno.recode html
get_b_se html
get_pve_se html
get_sdy html
gif html
grid2d html
h2.jags html
h2G html
h2GE html
h2_mzdz html
h2l html
hap html
hap.control html
hap.em html
hap.score html
hg18 html
hg19 html
hg38 html
hmht.control html
htr html
hwe html
hwe.cc html
hwe.hardy html
hwe.jags html
inv_chr_pos_a1_a2 html
invnormal html
ixy html
kin.morgan html
klem html
labelManhattan html
log10p html
log10pvalue html
logp html
makeped html
masize html
metap html
metareg html
mht.control html
mhtplot html
mhtplot.trunc html
mhtplot2 html
mia html
miamiplot html
miamiplot2 html
mr html
mr_forestplot html
mtdt html
mtdt2 html
muvar html
mvmeta html
pbsize html
pbsize2 html
pedtodot html
pedtodot_verbatim html
pfc html
pfc.sim html
pgc html
plot.hap.score html
print.hap.score html
pvalue html
qqfun html
qqunif html
qtl2dplot html
qtl2dplotly html
qtl3dplotly html
qtlClassifier html
read.ms.output html
revStrand html
runshinygap html
s2k html
sentinels html
snptest_sample html
tscc html
whscore html
xy html
** 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
* creating tarball
packaged installation of ‘gap’ as ‘gap_1.5-3_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (gap)