* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘phangorn’ ...
** package ‘phangorn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7GbI5O/R.INSTALL2bf29031a6396e/phangorn/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dist.c -o dist.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dupAtomMat.cpp -o dupAtomMat.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fitch64.cpp -o fitch64.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ml.c -o ml.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phangorn.c -o phangorn.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phangorn_utils.cpp -o phangorn_utils.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sankoff.c -o sankoff.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sprdist.c -o sprdist.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o phangorn.so RcppExports.o dist.o dupAtomMat.o fitch64.o ml.o phangorn.o phangorn_utils.o sankoff.o sprdist.o -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/Rtmp7GbI5O/R.INSTALL2bf29031a6396e/phangorn/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7GbI5O/R.INSTALL2bf29031a6396e/phangorn/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7GbI5O/R.INSTALL2bf29031a6396e/phangorn/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-phangorn/00new/phangorn/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘phangorn’
finding HTML links ... done
Ancestors html
CI html
Laurasiatherian html
NJ html
SH.test html
SOWH.test html
add.tips html
addConfidences html
add_ci html
add_edge_length html
allTrees html
ancestral.pml html
as.networx html
as.phyDat html
as.splits html
bab html
baseFreq html
bootstrap.pml html
chloroplast html
cladePar html
coalSpeciesTree html
codonTest html
consensusNet html
cophenetic.networx html
delta.score html
densiTree html
designTree html
dfactorial html
discrete.gamma html
dist.hamming html
dist.p html
distanceHadamard html
dna2codon html
gap_as_state html
getClans html
hadamard html
identify.networx html
image.phyDat html
latag2n.phyDat html
lento html
mast html
maxCladeCred html
midpoint html
mites html
modelTest html
neighborNet html
nni html
parsimony html
phangorn-internal html
phangorn-package html
phyDat html
plot.ancestral html
plot.networx html
plot.pml html
plotBS html
pml html
pml.control html
pml.fit html
pmlCluster html
pmlMix html
pmlPart html
pml_bb html
read.nexus.partitions html
read.nexus.splits html
read.phyDat html
reexports html
simSeq html
splitsNetwork html
superTree html
transferBootstrap html
treedist html
upgma html
write.ancestral html
write.pml html
writeDist html
yeast html
*** copying figures
** 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 (phangorn)