* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bio3d’ ...
** package ‘bio3d’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpT7kEBt/R.INSTALL39528265dadf45/bio3d/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 gzstream.cpp -o gzstream.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 init.c -o init.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 read_cif.cpp -o read_cif.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 read_crd.cpp -o read_crd.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 read_pdb.cpp -o read_pdb.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 read_prmtop.cpp -o read_prmtop.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -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 utils.cpp -o utils.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bio3d.so RcppExports.o gzstream.o init.o read_cif.o read_crd.o read_pdb.o read_prmtop.o utils.o -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpT7kEBt/R.INSTALL39528265dadf45/bio3d/src'
make[1]: Entering directory '/tmp/RtmpT7kEBt/R.INSTALL39528265dadf45/bio3d/src'
make[1]: Leaving directory '/tmp/RtmpT7kEBt/R.INSTALL39528265dadf45/bio3d/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bio3d/00new/bio3d/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 ‘bio3d’
finding HTML links ... done
aa.index html
aa.table html
aa123 html
aa2index html
aa2mass html
aanma.pdb html
aanma.pdbs html
aln2html html
angle.xyz html
as.fasta html
as.pdb html
as.select html
atom.index html
atom.select html
atom2ele html
atom2mass html
atom2xyz html
basename.pdb html
bhattacharyya html
binding.site html
bio3d.package html
biounit html
blast.pdb html
bounds html
bounds.sse html
bwr.colors html
cat.pdb html
chain.pdb html
check.utility html
clean.pdb html
cmap html
cna html
cnapath html
com html
combine.select html
community.aln html
community.tree html
consensus html
conserv html
convert.pdb html
core.cmap html
core.find html
cov.nma html
covsoverlap html
dccm html
dccm.enma html
dccm.gnm html
dccm.nma html
dccm.pca html
dccm.xyz html
deformation.nma html
diag.ind html
difference.vector html
dist.xyz html
dm html
dssp html
elements html
entropy html
example.data html
filter.cmap html
filter.dccm html
filter.identity html
filter.rmsd html
fit.xyz html
fluct.nma html
formula2mass html
gap.inspect html
geostas html
get.pdb html
get.seq html
gnm html
hclustplot html
hmmer html
identify.cna html
inner.prod html
inspect.connectivity html
is.gap html
is.mol2 html
is.pdb html
is.select html
is.xyz html
layout.cna html
lbio3d html
load.enmff html
mask.dccm html
mktrj html
motif.find html
mustang html
network.amendment html
nma html
nma.pdb html
nma.pdbs html
normalize.vector html
orient.pdb html
overlap html
pairwise html
pca html
pca.array html
pca.pdbs html
pca.tor html
pca.xyz html
pdb.annotate html
pdb2aln html
pdb2aln.ind html
pdb2sse html
pdbaln html
pdbfit html
pdbs2pdb html
pdbs2sse html
pdbseq html
pdbsplit html
pfam html
plot.bio3d html
plot.cmap html
plot.cna html
plot.core html
plot.dccm html
plot.dmat html
plot.enma html
plot.fasta html
plot.fluct html
plot.geostas html
plot.hmmer html
plot.matrix.loadings html
plot.nma html
plot.pca html
plot.pca.loadings html
plot.rmsip html
print.cna html
print.core html
print.fasta html
print.xyz html
project.pca html
prune.cna html
pymol html
read.all html
read.cif html
read.crd html
read.crd.amber html
read.crd.charmm html
read.dcd html
read.fasta html
read.fasta.pdb html
read.mol2 html
read.ncdf html
read.pdb html
read.pdcBD html
read.pqr html
read.prmtop html
rgyr html
rle2 html
rmsd html
rmsf html
rmsip html
sdENM html
seq2aln html
seqaln html
seqaln.pair html
seqbind html
seqidentity html
setup.ncore html
sip html
sse.bridges html
store.atom html
struct.aln html
torsion.pdb html
torsion.xyz html
trim.mol2 html
trim.pdb html
trim.pdbs html
trim.xyz html
unbound html
uniprot html
var.xyz html
vec2resno html
vmd.cna html
vmd_colors html
wrap.tor html
write.crd html
write.fasta html
write.mol2 html
write.ncdf html
write.pdb html
write.pir html
write.pqr 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 (bio3d)