krauseNiazi2019Analyses: Reproducible analysis for tailfindr paper

processx 3.3.1

Fix a crash on Windows, when a connection that has a pending read internally is finalized.

processx 3.3.0

process can now redirect the standard error to the standard output, via specifying stderr = "2>&1". This works both with files and pipes.
run() can now redirect the standard error to the standard output, via the new stderr_to_stdout argument.
The $kill() and $kill_tree() methods get a close_connection = TRUE argument that closes all pipe connections of the process.
run() now always kills the process (and its process tree if cleanup_tree is TRUE) before exiting. This also closes all pipe connections (#149).

processx 3.2.1

processx does not depend on assertthat now, and the crayon package is now an optional dependency.

processx 3.2.0

New process$kill_tree() method, and new cleanup_tree arguments in run() and process$new(), to clean up the process tree rooted at a processx process. (#139, #143).
New process$interupt() method to send an interrupt to a process, SIGINT on Unix, CTRL+C on Windows (#127).
New stdin argument in process$new() to support writing to the standard input of a process (#27, #114).
New connections argument in process$new() to support passing extra connections to the child process, in addition to the standard streams.
New poll_connection argument to process$new(), an extra connection that can be used to poll the process, even if stdout and stderr are not pipes (#125).
poll() now works with connections objects, and they can be mixed with process objects (#121).
New env argument in run() and process$new(), to set the environment of the child process, optionally (#117, #118).
Removed the $restart() method, because it was less useful than expected, and hard to maintain (#116).
New conn_set_stdout() and conn_set_stderr() to set the standard output or error of the calling process.
New conn_disable_inheritance() to disable stdio inheritance. It is suggested that child processes call this immediately after starting, so the file handles are not inherited further.
Fixed a signal handler bug on Unix that marked the process as finished, even if it has not (d221aa1f).
Fixed a bug that occasionally caused crashes in wait(), on Unix (#138).
When run() is interrupted, no error message is printed, just like for interruption of R code in general. The thrown condition now also has the interrupt class (#148).

processx 3.1.0

Fix interference with the parallel package, and other packages that redefine the SIGCHLD signal handler on Unix. If the processx signal handler is overwritten, we might miss the exit status of some processes (they are set to NA).
run() and process$new() allow specifying the working directory of the process (#63).
Make the debugme package an optional dependency (#74).
processx is now compatible with R 3.1.x.
Allow polling more than 64 connections on Windows, by using IOCP instead of WaitForMultipleObjects() (#81, #106).
Fix a race condition on Windows, when creating named pipes for stdout or stderr. The client sometimes didn't wait for the server, and processx failed with ERROR_PIPE_BUSY (231, All pipe instances are busy).

processx 3.0.3

Fix a crash on windows when trying to run a non-existing command (#90)
Fix a race condition in process$restart()
run() and process$new() do not support the commandline argument any more, because process cleanup is error prone with an intermediate shell. (#88)
processx process objects no longer use R connection objects, because the R connection API was retroactive made private by R-core processx uses its own connection class now to manage standard output and error of the process.
The encoding of the standard output and error can be specified now, and processx re-encodes stdout and stderr in UTF-8.
Cloning of process objects is disables now, as it is likely that it causes problems (@wch).
supervise option to kill child process if R crashes (@wch).
Add get_output_file and get_error_file, has_output_connection() and has_error_connection() methods (@wch).
stdout and stderr default to NULL now, i.e. they are discarded (@wch).
Fix undefined behavior when stdout/stderr was read out after the process was already finalized, on Unix.
run(): Better message on interruption, kill process when interrupted.
Unix: better kill count on unloading the package.
Unix: make wait() work when SIGCHLD is not delivered for some reason.
Unix: close inherited file descriptors more conservatively.
Fix a race condition and several memory leaks on Windows.
Fixes when running under job control that does not allow breaking away from the job, on Windows.