krauseNiazi2019Analyses: Reproducible analysis for tailfindr paper

callr 3.2.0

r(), rcmd() and rscript() can now redirect the standard error of the subprocess its standard output. This allows to keep them correctly interleaved. For this, you need to either set the stderr argument to the special string "2>&1", or to the same output file as specified for stdout.
r(), rcmd() and rscript() now pass ... arguments to processx::run(). r_bg() and rcmd_bg() pass ... arguments to the processx::process constructor. For r_process, rcmd_process and rscript_process extra arguments can be specified as options$extra, these are also passed to the processx::process constructor (#100).

r(), r_bg(), etc. now handle messages from the cliapp package properly. They used to make the R session exit.
Better default for the repos option in callr subprocesses. callr no longer creates duplicate "CRAN" entries. By default the new default_repos() function is used to set repos in the subprocess.

New rscript() function and rscript_process class to execute R scripts via Rscript (#40, #81).
Library paths are now correctly set up for system() (and similar) calls from the callr subprocesses (#83, #84).
Pass options("repos") to the child process as is, without checking. Closes #82.
r_session$run_with_output() now returns an S3 object with class callr_session_result.
r_session$run*() handle interrupts properly. It tries to interrupt the background process fist, kills it if it is not interruptable, and then re-throws the interrupt condition, going back to the top level prompt if the re-thrown condition is un-caught.

pkgdown web site at https://callr.r-lib.org (#52, #53).
callr users .Renviron files now (and R_ENVIRON_USER as well), but overrides the library path, as requested in r(), etc. (#30).
callr now handles the case when the subprocess calls quit().
callr now uses the processx package, instead of embedded code, to create and control processes.

Fix a bug with R-devel, caused by the change on 2018-02-08: https://github.com/wch/r-source/commit/924582943706100e88a11d6bb0585d25779c91f5 #37, #38
Fix a race condition on Windows, when creating named pipes for stdout or stderr. The client sometimes didn't wait for the server, and callr failed with ERROR_PIPE_BUSY (231, All pipe instances are busy).

Run R or R CMD * in the background, see r_bg(), rcmd_bg(), and also r_process and rcmd_process
The defaults for r() are safer now, the match the defaults of r_safe(). r_safe() is kept for compatibility. r_copycat() has the old r() defaults.
The defaults for rcmd() are safer now, the match the defaults of rcmd_safe(). rcmd_safe() is kept for compatibility. rcmd_copycat() has the old rcmd() defaults.
Support block callbacks, in addition to line callbacks. Block callbacks are called for arbitrary chunks of output, even without a newline
Add spinner argument to show a spinner in r() or rcmd()
Support timeouts, via the timeout argument
Fix bug when stdout and stderr are redirected to the same file
rcmd_safe_env() to allow extending the environment variables set in safe mode
rcmd() gets a fail_on_status argument
rcmd() gets an echo argument to potentially show the command to be run on the screen (#15)
rcmd() gets a wd argument to set the working directory