* 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 13.3.0-1) 13.3.0’
using C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’
using C++11
make[1]: Entering directory '/tmp/RtmppJC6pe/R.INSTALLb3626234eefb7/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/RtmppJC6pe/R.INSTALLb3626234eefb7/bio3d/src'
make[1]: Entering directory '/tmp/RtmppJC6pe/R.INSTALLb3626234eefb7/bio3d/src'
make[1]: Leaving directory '/tmp/RtmppJC6pe/R.INSTALLb3626234eefb7/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)