* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘taxonomizr’ ...
** package ‘taxonomizr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/Rtmp0dXxz1/R.INSTALL16b4757b94d31d/taxonomizr/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 taxaTrim.c -o taxaTrim.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 taxonomizr-init.c -o taxonomizr-init.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o taxonomizr.so taxaTrim.o taxonomizr-init.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp0dXxz1/R.INSTALL16b4757b94d31d/taxonomizr/src'
make[1]: Entering directory '/tmp/Rtmp0dXxz1/R.INSTALL16b4757b94d31d/taxonomizr/src'
make[1]: Leaving directory '/tmp/Rtmp0dXxz1/R.INSTALL16b4757b94d31d/taxonomizr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-taxonomizr/00new/taxonomizr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘taxonomizr’
    finding HTML links ... done
    accessionToTaxa                         html  
    condenseTaxa                            html  
    getAccession2taxid                      html  
    getAccessions                           html  
    getCommon                               html  
    getDescendants                          html  
    getId                                   html  
    getId2                                  html  
    getNamesAndNodes                        html  
    getRawTaxonomy                          html  
    getTaxonomy                             html  
    getTaxonomy2                            html  
    lastNotNa                               html  
    makeNewick                              html  
    normalizeTaxa                           html  
    prepareDatabase                         html  
    read.accession2taxid                    html  
    read.names                              html  
    read.names.sql                          html  
    read.nodes                              html  
    read.nodes.sql                          html  
    resumableDownload                       html  
    streamingRead                           html  
    taxonomizr-package                      html  
    taxonomizrSwitch                        html  
    topoSort                                html  
    trimTaxa                                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 (taxonomizr)