* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rbiom’ ...
** package ‘rbiom’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLQIN15/R.INSTALL4b32c571406b6/rbiom/src'
gcc-14 -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 alpha_div.c -o alpha_div.o
gcc-14 -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 beta_div.c -o beta_div.o
gcc-14 -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-14 -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 pthreads.c -o pthreads.o
gcc-14 -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 rarefy.c -o rarefy.o
gcc-14 -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 read_tree.c -o read_tree.o
gcc-14 -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 unifrac.c -o unifrac.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rbiom.so alpha_div.o beta_div.o init.o pthreads.o rarefy.o read_tree.o unifrac.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLQIN15/R.INSTALL4b32c571406b6/rbiom/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLQIN15/R.INSTALL4b32c571406b6/rbiom/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLQIN15/R.INSTALL4b32c571406b6/rbiom/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rbiom/00new/rbiom/libs
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘rbiom’
finding HTML links ... done
adiv_boxplot html
adiv_corrplot html
adiv_matrix html
adiv_stats html
adiv_table html
as.list.rbiom html
as.matrix.rbiom html
as_rbiom html
babies html
bdiv_boxplot html
bdiv_clusters html
bdiv_corrplot html
bdiv_heatmap html
bdiv_ord_plot html
bdiv_ord_table html
bdiv_stats html
bdiv_table html
bdply html
biom_merge html
distmat_ord_table html
distmat_stats html
documentation_biom.rbiom html
documentation_clusters html
documentation_cmp html
documentation_default html
documentation_dist_test html
documentation_heatmap html
documentation_plot_return html
documentation_rank.2 html
documentation_rank.NULL html
documentation_return.biom html
documentation_taxa.4 html
gems html
glimpse.rbiom html
hmp50 html
modify_metadata html
plot_heatmap html
pull.rbiom html
rare_corrplot html
rare_multiplot html
rare_stacked html
rarefy html
rarefy_cols html
rbiom-deprecated html
rbiom-package html
rbiom_objects html
read_biom html
read_fasta html
read_tree html
reexports html
sample_sums html
slice_metadata html
speed html
stats_boxplot html
stats_corrplot html
stats_table html
subset html
taxa_boxplot html
taxa_clusters html
taxa_corrplot html
taxa_heatmap html
taxa_map html
taxa_matrix html
taxa_stacked html
taxa_stats html
taxa_sums html
tree_subset html
with html
write_biom html
*** copying figures
** 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 (rbiom)