* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘adegenet’ ...
** package ‘adegenet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmprZqEps/R.INSTALL11dda63d7455eb/adegenet/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 GLfunctions.c -o GLfunctions.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 adesub.c -o adesub.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 monmonier-utils.c -o monmonier-utils.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 sharedAll.c -o sharedAll.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 snpbin.c -o snpbin.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o adegenet.so GLfunctions.o adesub.o init.o monmonier-utils.o sharedAll.o snpbin.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmprZqEps/R.INSTALL11dda63d7455eb/adegenet/src'
make[1]: Entering directory '/tmp/RtmprZqEps/R.INSTALL11dda63d7455eb/adegenet/src'
make[1]: Leaving directory '/tmp/RtmprZqEps/R.INSTALL11dda63d7455eb/adegenet/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘adegenet’
finding HTML links ... done
AIC.snapclust html
AICc html
BIC.snapclust html
H3N2 html
HWE html
Hs html
Hs.test html
KIC html
SNPbin html
accessors html
adegenet.package html
as-methods html
as.SNPbin html
as.genlight html
ascore html
auxil html
chooseCN html
colorplot html
compoplot html
coords.monmonier html
dapc html
dapcGraphics html
dapcIllus html
df2genind html
finding level-2 HTML links ... done
dist.genpop html
doc_C_routines html
eHGDP html
export_to_mvmapper html
fasta2DNAbin html
fasta2genlight html
find.clusters html
gengraph html
genind html
genind2df html
genind2genpop html
genlight html
genpop html
glAux html
glPca html
glPlot html
glSim html
haploGen html
hierarchy-methods html
hybridize html
hybridtoy html
import2genind html
inbreeding html
isPoly html
loadingplot html
makefreq html
microbov html
minorAllele html
monmonier html
mutations html
nancycats html
new.genind html
REDIRECT:topic Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/help/genind.html
new.genpop html
REDIRECT:topic Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/help/genpop.html
old2new html
pairDist html
population-methods html
propShared html
propTyped html
read.PLINK html
read.fstat html
read.genepop html
read.genetix html
read.snp html
read.structure html
repool html
rupica html
scaleGen html
selpopsize html
seploc html
seppop html
seqTrack html
sequences html
servers html
showmekittens html
sim2pop html
snapclust html
snapclust.choose.k html
snpposi html
snpzip html
spca html
spca.rtests html
spcaIllus html
spca_randtest html
strata-methods html
swallowtails html
tab html
truenames html
virClasses html
web html
xvalDapc 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 (adegenet)