* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pegas’ ...
** package ‘pegas’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3VjvuU/R.INSTALL21b6835579aa2b/pegas/src'
gcc-14 -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 mst.c -o mst.o
gcc-14 -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 pegas.c -o pegas.o
gcc-14 -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 readVCFbin.c -o readVCFbin.o
readVCFbin.c: In function ‘read_bin_pegas’:
readVCFbin.c:18:13: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable]
18 | int sz, retval;
| ^~~~~~
gcc-14 -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 summary_loci_pegas.c -o summary_loci_pegas.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pegas.so mst.o pegas.o readVCFbin.o summary_loci_pegas.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3VjvuU/R.INSTALL21b6835579aa2b/pegas/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3VjvuU/R.INSTALL21b6835579aa2b/pegas/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3VjvuU/R.INSTALL21b6835579aa2b/pegas/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pegas/00new/pegas/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pegas’
finding HTML links ... done
F234 html
Fst html
LD html
LDscan html
MMD html
R2.test html
VCFloci html
all.equal.haploNet html
alleles2loci html
allelicrichness html
amova html
bind.loci html
by.loci html
conversion html
cophenetic.haploNet html
diffHaplo html
dist.asd html
dist.hamming html
edit.loci html
geoTrans html
geod html
hap.div html
haploFreq html
haploNet html
haplotype html
haplotype.loci html
heterozygosity html
hw.test html
jaguar html
mjn html
mst html
mutations html
na.omit.loci html
nuc.div html
options_themes_haploNet html
pegas-package html
plotNetMDS html
read.gtx html
read.loci html
read.vcf html
replot html
rr.test html
site.spectrum html
stairway html
subset.haplotype html
summary.loci html
sw html
tajima.test html
theta.h html
theta.k html
theta.msat html
theta.s html
theta.tree html
utilities html
write.loci 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
* DONE (pegas)