Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gomez.nitrogen
> ### Title: Soil nitrogen at three times for eight fertilizer treatments
> ### Aliases: gomez.nitrogen
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(agridat)
> 
> data(gomez.nitrogen)
> dat <- gomez.nitrogen
> 
> # Note the depletion of nitrogen over time (stage)
> libs(HH)
Installing package into ‘/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd’
(as ‘lib’ is unspecified)
also installing the dependencies ‘checkmate’, ‘htmlwidgets’, ‘rstudioapi’, ‘commonmark’, ‘httpuv’, ‘later’, ‘promises’, ‘sourcetools’, ‘xtable’, ‘htmlTable’, ‘gridExtra’, ‘leaps’, ‘shiny’, ‘Hmisc’, ‘Rmpfr’

* installing *source* package ‘checkmate’ ...
** this is package ‘checkmate’ version ‘2.3.4’
** package ‘checkmate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/RtmpKU0oLi/R.INSTALL2059bc2ae37083/checkmate/src'
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c all_missing.c -o all_missing.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c any_infinite.c -o any_infinite.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c any_missing.c -o any_missing.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c any_nan.c -o any_nan.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c checks.c -o checks.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c find_nchar.c -o find_nchar.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c guess_type.c -o guess_type.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c helper.c -o helper.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c integerish.c -o integerish.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c is_sorted.c -o is_sorted.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c qassert.c -o qassert.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c which_first.c -o which_first.o
gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpKU0oLi/R.INSTALL2059bc2ae37083/checkmate/src'
make[1]: Entering directory '/tmp/RtmpKU0oLi/R.INSTALL2059bc2ae37083/checkmate/src'
make[1]: Leaving directory '/tmp/RtmpKU0oLi/R.INSTALL2059bc2ae37083/checkmate/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-checkmate/00new/checkmate/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (checkmate)
* installing *source* package ‘htmlwidgets’ ...
** this is package ‘htmlwidgets’ version ‘1.6.4’
** package ‘htmlwidgets’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmlwidgets)
* installing *source* package ‘rstudioapi’ ...
** this is package ‘rstudioapi’ version ‘0.18.0’
** package ‘rstudioapi’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rstudioapi)
* installing *source* package ‘commonmark’ ...
** this is package ‘commonmark’ version ‘2.0.0’
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/Rtmp7qkjNz/R.INSTALL2094134bc51c20/commonmark/src'
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions.c -o extensions.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c wrapper.c -o wrapper.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/cmark.c -o cmark/cmark.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/node.c -o cmark/node.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/iterator.c -o cmark/iterator.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/blocks.c -o cmark/blocks.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/inlines.c -o cmark/inlines.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/scanners.c -o cmark/scanners.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/utf8.c -o cmark/utf8.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/buffer.c -o cmark/buffer.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/references.c -o cmark/references.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/render.c -o cmark/render.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/man.c -o cmark/man.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/xml.c -o cmark/xml.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/html.c -o cmark/html.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/commonmark.c -o cmark/commonmark.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/latex.c -o cmark/latex.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/houdini_href_e.c -o cmark/houdini_href_e.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/houdini_html_e.c -o cmark/houdini_html_e.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/houdini_html_u.c -o cmark/houdini_html_u.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/cmark_ctype.c -o cmark/cmark_ctype.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/arena.c -o cmark/arena.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/linked_list.c -o cmark/linked_list.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/plugin.c -o cmark/plugin.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/registry.c -o cmark/registry.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/syntax_extension.c -o cmark/syntax_extension.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/plaintext.c -o cmark/plaintext.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/footnotes.c -o cmark/footnotes.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cmark/map.c -o cmark/map.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/autolink.c -o extensions/autolink.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/core-extensions.c -o extensions/core-extensions.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/ext_scanners.c -o extensions/ext_scanners.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/strikethrough.c -o extensions/strikethrough.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/table.c -o extensions/table.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/tagfilter.c -o extensions/tagfilter.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c extensions/tasklist.c -o extensions/tasklist.o
gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o commonmark.so extensions.o init.o wrapper.o -Lcmark -lstatcmark -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp7qkjNz/R.INSTALL2094134bc51c20/commonmark/src'
make[1]: Entering directory '/tmp/Rtmp7qkjNz/R.INSTALL2094134bc51c20/commonmark/src'
make[1]: Leaving directory '/tmp/Rtmp7qkjNz/R.INSTALL2094134bc51c20/commonmark/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-commonmark/00new/commonmark/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (commonmark)
* installing *source* package ‘later’ ...
** this is package ‘later’ version ‘1.4.8’
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
using C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/RtmpVcYXuu/R.INSTALL20d115ef551f8/later/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c callback_registry.cpp -o callback_registry.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c debug.cpp -o debug.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fd.cpp -o fd.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/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++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c later.cpp -o later.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c later_posix.cpp -o later_posix.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c later_win32.cpp -o later_win32.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c timer_posix.cpp -o timer_posix.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c timestamp_unix.cpp -o timestamp_unix.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c timestamp_win32.cpp -o timestamp_win32.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c tinycthread.c -o tinycthread.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES  -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c wref.c -o wref.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o later.so RcppExports.o callback_registry.o debug.o fd.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o wref.o -pthread -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpVcYXuu/R.INSTALL20d115ef551f8/later/src'
make[1]: Entering directory '/tmp/RtmpVcYXuu/R.INSTALL20d115ef551f8/later/src'
make[1]: Leaving directory '/tmp/RtmpVcYXuu/R.INSTALL20d115ef551f8/later/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-later/00new/later/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (later)
* installing *source* package ‘sourcetools’ ...
** this is package ‘sourcetools’ version ‘0.1.7-2’
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
using C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/RtmpOYcyH1/R.INSTALL21445c66ad8432/sourcetools/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Reader.cpp -o Reader.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Tokenizer.cpp -o Tokenizer.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sourcetools-init.c -o sourcetools-init.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpOYcyH1/R.INSTALL21445c66ad8432/sourcetools/src'
make[1]: Entering directory '/tmp/RtmpOYcyH1/R.INSTALL21445c66ad8432/sourcetools/src'
make[1]: Leaving directory '/tmp/RtmpOYcyH1/R.INSTALL21445c66ad8432/sourcetools/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-sourcetools/00new/sourcetools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (sourcetools)
* installing *source* package ‘xtable’ ...
** this is package ‘xtable’ version ‘1.8-8’
** package ‘xtable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xtable)
* installing *source* package ‘gridExtra’ ...
** this is package ‘gridExtra’ version ‘2.3’
** package ‘gridExtra’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gridExtra)
* installing *source* package ‘leaps’ ...
** this is package ‘leaps’ version ‘3.2’
** package ‘leaps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
using Fortran compiler: ‘GNU Fortran (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/RtmptHT5oe/R.INSTALL216d8655b662e9/leaps/src'
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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
gfortran-16  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c leaps.f -o leaps.o
gfortran-16  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c leapshdr.f -o leapshdr.o
gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o leaps.so init.o leaps.o leapshdr.o -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmptHT5oe/R.INSTALL216d8655b662e9/leaps/src'
make[1]: Entering directory '/tmp/RtmptHT5oe/R.INSTALL216d8655b662e9/leaps/src'
make[1]: Leaving directory '/tmp/RtmptHT5oe/R.INSTALL216d8655b662e9/leaps/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-leaps/00new/leaps/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (leaps)
* installing *source* package ‘Rmpfr’ ...
** this is package ‘Rmpfr’ version ‘1.1-2’
** package ‘Rmpfr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-16
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc-16 accepts -g... yes
checking for gcc-16 option to enable C11 features... none needed
checking how to run the C preprocessor... gcc-16 -E
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for mpfr.h... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
checking for mpfr_init in -lmpfr... yes
checking for mpfr_digamma in -lmpfr... yes
checking size of mp_limb_t... 8
checking size of mpfr_prec_t... 8
checking size of mpfr_exp_t... 8
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/Rtmp2vfpMO/R.INSTALL217c484fd17d64/Rmpfr/src'
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DHAVE_CONFIG_H  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c Ops.c -o Ops.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DHAVE_CONFIG_H  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c Summary.c -o Summary.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DHAVE_CONFIG_H  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c convert.c -o convert.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DHAVE_CONFIG_H  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DHAVE_CONFIG_H  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c utils.c -o utils.o
gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o Rmpfr.so Ops.o Summary.o convert.o init.o utils.o -lmpfr -lgmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp2vfpMO/R.INSTALL217c484fd17d64/Rmpfr/src'
make[1]: Entering directory '/tmp/Rtmp2vfpMO/R.INSTALL217c484fd17d64/Rmpfr/src'
make[1]: Leaving directory '/tmp/Rtmp2vfpMO/R.INSTALL217c484fd17d64/Rmpfr/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-Rmpfr/00new/Rmpfr/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Rmpfr’
Creating a new generic function for ‘cbind’ in package ‘Rmpfr’
Creating a new generic function for ‘rbind’ in package ‘Rmpfr’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Rmpfr’
in method for ‘show’ with signature ‘"integrateR"’: no definition for class “integrateR”
Creating a new generic function for ‘pmin’ in package ‘Rmpfr’
Creating a new generic function for ‘pmax’ in package ‘Rmpfr’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘beta’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘lbeta’ from package ‘base’ in package ‘Rmpfr’
** help
*** installing help indices
** 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 (Rmpfr)
* installing *source* package ‘promises’ ...
** this is package ‘promises’ version ‘1.5.0’
** package ‘promises’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (promises)
* installing *source* package ‘htmlTable’ ...
** this is package ‘htmlTable’ version ‘2.5.0’
** package ‘htmlTable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmlTable)
* installing *source* package ‘httpuv’ ...
** this is package ‘httpuv’ version ‘1.6.17’
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** using staged installation
** Using libuv found by pkg-config in /usr
** PKG_CFLAGS=
** PKG_LIBS=-luv -lpthread -ldl -lrt -lm
** libs
using C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
using C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
make[1]: Entering directory '/tmp/RtmpIH18DD/R.INSTALL21f70c45486787/httpuv/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c callback.cpp -o callback.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c callbackqueue.cpp -o callbackqueue.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filedatasource-unix.cpp -o filedatasource-unix.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filedatasource-win.cpp -o filedatasource-win.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fs.cpp -o fs.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c gzipdatasource.cpp -o gzipdatasource.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c http.cpp -o http.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c httprequest.cpp -o httprequest.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c httpresponse.cpp -o httpresponse.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c httpuv.cpp -o httpuv.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c md5.c -o md5.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mime.cpp -o mime.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c socket.cpp -o socket.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c staticpath.cpp -o staticpath.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c thread.cpp -o thread.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c timegm.cpp -o timegm.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c utils.cpp -o utils.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c uvutil.cpp -o uvutil.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c webapplication.cpp -o webapplication.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c websockets-base.cpp -o websockets-base.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c websockets-hixie76.cpp -o websockets-hixie76.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c websockets-hybi03.cpp -o websockets-hybi03.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c websockets-ietf.cpp -o websockets-ietf.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c websockets.cpp -o websockets.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c winutils.cpp -o winutils.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c http-parser/http_parser.c -o http-parser/http_parser.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sha1/sha1.c -o sha1/sha1.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -pthread -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/later/include' -I'/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2 -Wall -pedantic -mtune=native   -c base64/base64.cpp -o base64/base64.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o -luv -lpthread -ldl -lrt -lm ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpIH18DD/R.INSTALL21f70c45486787/httpuv/src'
make[1]: Entering directory '/tmp/RtmpIH18DD/R.INSTALL21f70c45486787/httpuv/src'
make[1]: Leaving directory '/tmp/RtmpIH18DD/R.INSTALL21f70c45486787/httpuv/src'
installing to /tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/00LOCK-httpuv/00new/httpuv/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (httpuv)
ERROR: dependencies ‘rpart’, ‘foreign’ are not available for package ‘Hmisc’
Perhaps try a variation of:
install.packages(c('rpart', 'foreign'))
* removing ‘/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/Hmisc’
Warning in install.packages(p) :
  installation of package ‘Hmisc’ had non-zero exit status
* installing *source* package ‘shiny’ ...
** this is package ‘shiny’ version ‘1.13.0’
** package ‘shiny’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (shiny)
ERROR: dependency ‘Hmisc’ is not available for package ‘HH’
Perhaps try a variation of:
install.packages('Hmisc')
* removing ‘/tmp/Rtmp3aSPRk/RLIBS_1fb4325e0c75bd/HH’
Warning in install.packages(p) :
  installation of package ‘HH’ had non-zero exit status
Error in library(p, character.only = TRUE) : 
  there is no package called ‘HH’
Calls: libs -> library
Execution halted