Error(s) in re-building vignettes:
--- re-building ‘checkpoint.Rmd’ using rmarkdown
* installing *source* package ‘darts’ ...
staged installation is only possible with locking
** using non-staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXSSB9V/working_dir/RtmpPINA8n/R.INSTALL5ae66768aa60/darts/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c darts.c -o darts.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o darts.so darts.o
make[1]: Leaving directory '/tmp/RtmpXSSB9V/working_dir/RtmpPINA8n/R.INSTALL5ae66768aa60/darts/src'
make[1]: Entering directory '/tmp/RtmpXSSB9V/working_dir/RtmpPINA8n/R.INSTALL5ae66768aa60/darts/src'
make[1]: Leaving directory '/tmp/RtmpXSSB9V/working_dir/RtmpPINA8n/R.INSTALL5ae66768aa60/darts/src'
installing to /tmp/RtmpXSSB9V/working_dir/Rtmptr0ewh/.checkpoint/2017-04-01/lib/x86_64-pc-linux-gnu/4.0.0/darts/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (darts)
Warning in file(con, "w") :
  cannot open file '/tmp/RtmpXSSB9V/working_dir/Rtmptr0ewh/rmarkdown-str423e1f8cde1b.html': No such file or directory
Error: processing vignette 'checkpoint.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘checkpoint.Rmd’

--- re-building ‘managing-checkpoint-archives.Rmd’ using rmarkdown

checkpoint: Part of the Reproducible R Toolkit from Microsoft
https://mran.microsoft.com/documents/rro/reproducibility/
Scanning for packages used in this project
- Discovered 1 packages
Installing packages used in this project 
 - Installing 'darts'
darts
* installing *source* package ‘darts’ ...
staged installation is only possible with locking
** using non-staged installation
** libs
make[1]: Entering directory '/tmp/RtmpXSSB9V/working_dir/Rtmp1ltLpp/R.INSTALL6ae7732c685f/darts/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c darts.c -o darts.o
clang -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o darts.so darts.o
make[1]: Leaving directory '/tmp/RtmpXSSB9V/working_dir/Rtmp1ltLpp/R.INSTALL6ae7732c685f/darts/src'
make[1]: Entering directory '/tmp/RtmpXSSB9V/working_dir/Rtmp1ltLpp/R.INSTALL6ae7732c685f/darts/src'
make[1]: Leaving directory '/tmp/RtmpXSSB9V/working_dir/Rtmp1ltLpp/R.INSTALL6ae7732c685f/darts/src'
installing to /tmp/RtmpXSSB9V/working_dir/Rtmp7UGJgN/.checkpoint/2015-04-26/lib/x86_64-pc-linux-gnu/4.0.0/darts/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (darts)
checkpoint process complete
---
--- finished re-building ‘managing-checkpoint-archives.Rmd’

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

Error: Vignette re-building failed.
Execution halted