Error(s) in re-building vignettes:
--- re-building ‘ALA4R.Rmd’ using rmarkdown
Installing package into '/data/gannet/ripley/R/packages/tests-devel/ALA4R.Rcheck'
(as 'lib' is unspecified)
also installing the dependencies 'fastmatch', 'phangorn'

trying URL 'http://cran.us.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz'
Content type 'application/x-gzip' length 14290 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'http://cran.us.r-project.org/src/contrib/phangorn_2.7.1.tar.gz'
Content type 'application/x-gzip' length 1975903 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'http://cran.us.r-project.org/src/contrib/phytools_0.7-80.tar.gz'
Content type 'application/x-gzip' length 328187 bytes (320 KB)
==================================================
downloaded 320 KB

* installing *source* package ‘fastmatch’ ...
** package ‘fastmatch’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpCJOQrc/working_dir/RtmpFu66rs/R.INSTALL25c74826d0fa/fastmatch/src'
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration  -c ctapply.c -o ctapply.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration  -c fasthash.c -o fasthash.o
In file included from fasthash.c:19:
common.h:13:17: error: conflicting types for ‘R_xlen_t’
   13 | typedef R_len_t R_xlen_t;
      |                 ^~~~~~~~
In file included from common.h:8,
                 from fasthash.c:19:
/data/gannet/ripley/R/R-devel/include/Rinternals.h:72:23: note: previous declaration of ‘R_xlen_t’ was here
   72 |     typedef ptrdiff_t R_xlen_t;
      |                       ^~~~~~~~
make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:168: fasthash.o] Error 1
make[1]: Leaving directory '/tmp/RtmpCJOQrc/working_dir/RtmpFu66rs/R.INSTALL25c74826d0fa/fastmatch/src'
ERROR: compilation failed for package ‘fastmatch’
* removing ‘/data/gannet/ripley/R/packages/tests-devel/ALA4R.Rcheck/fastmatch’
ERROR: dependency ‘fastmatch’ is not available for package ‘phangorn’
* removing ‘/data/gannet/ripley/R/packages/tests-devel/ALA4R.Rcheck/phangorn’
ERROR: dependency ‘phangorn’ is not available for package ‘phytools’
* removing ‘/data/gannet/ripley/R/packages/tests-devel/ALA4R.Rcheck/phytools’

The downloaded source packages are in
	'/tmp/RtmpCJOQrc/working_dir/Rtmpn1tgwi/downloaded_packages'

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 153-155 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
there is no package called 'phytools'
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

Error: Vignette re-building failed.
Execution halted