Error in re-building vignettes:
  ...
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpvanNPz/R.INSTALLa3042751852d/MASS/src'
gcc -I/data/gannet/ripley/R/R-devel/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c MASS.c -o MASS.o
gcc -I/data/gannet/ripley/R/R-devel/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c lqs.c -o lqs.o
gcc -shared -L/usr/local/lib64 -o MASS.so MASS.o lqs.o
make[1]: Leaving directory '/tmp/RtmpvanNPz/R.INSTALLa3042751852d/MASS/src'
make[1]: Entering directory '/tmp/RtmpvanNPz/R.INSTALLa3042751852d/MASS/src'
make[1]: Leaving directory '/tmp/RtmpvanNPz/R.INSTALLa3042751852d/MASS/src'
installing to /tmp/Rtmp6rdyxf/.checkpoint/2017-04-01/lib/x86_64-pc-linux-gnu/3.5.0/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Scanning for packages used in this project
- Discovered 1 packages
Installing packages used in this project 
 - Installing 'MASS'
MASS
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpEwsdlN/R.INSTALLb94ba444c64/MASS/src'
gcc -I/data/gannet/ripley/R/R-devel/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c MASS.c -o MASS.o
gcc -I/data/gannet/ripley/R/R-devel/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c lqs.c -o lqs.o
gcc -shared -L/usr/local/lib64 -o MASS.so MASS.o lqs.o
make[1]: Leaving directory '/tmp/RtmpEwsdlN/R.INSTALLb94ba444c64/MASS/src'
make[1]: Entering directory '/tmp/RtmpEwsdlN/R.INSTALLb94ba444c64/MASS/src'
make[1]: Leaving directory '/tmp/RtmpEwsdlN/R.INSTALLb94ba444c64/MASS/src'
installing to /tmp/Rtmp6rdyxf/.checkpoint/2015-04-26/lib/x86_64-pc-linux-gnu/3.5.0/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
checkpoint process complete
---
Error: processing vignette 'managing-checkpoint-archives.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted