Remove rcppparallel

[koheiw]

This is a rather urgent upgrade of the package to avoid crashes caused by memory leaks (segment fault) in the old TBB library in RcppParallel. Since the package does not update the library, we need to link to the new version of the library ourselves.

The library is avaialble in rtools and windbuilder, so Windows users are not affected . Linux users need to install the library header themselves.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.52%. Comparing base (9b139ce) to head (ef2c1ae).

Additional details and impacted files

@@           Coverage Diff           @@
##           master      #47   +/-   ##
=======================================
  Coverage   99.51%   99.52%           
=======================================
  Files           4        5    +1     
  Lines         416      418    +2     
=======================================
+ Hits          414      416    +2     
  Misses          2        2           

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[rcannood]

Some minor comments. I'll run a revdepcheck in the meantime

[rcannood]

I'd be inclined to add a helper function, something along the lines of

getThreads <- function() {
  threads <- getOption("proxyC.threads", Sys.getenv("RCPP_PARALLEL_NUM_THREADS"))
  if (is.null(threads)) {
    threads <- -1L
  }
  threads <- as.integer(threads)
  if (length(threads != 1) || is.na(threads)) {
    stop("proxyC.threads must be an integer")
  }
  threads
}

I'd propose still supporting RCPP_PARALLEL_NUM_THREADS as an environment variable because otherwise this PR is a breaking change.

[koheiw]

That makes sense. I added getThreads() that also takes value from OMP_THREAD_LIMIT to stop using too many threads in CRAN tests.

[rcannood]

revdepcheck is ok!

── INSTALL ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 2 versions ──
Installing CRAN version of proxyC
Installing DEV version of proxyC
── CHECK ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 12 packages ──
✔ quanteda.textstats 0.96.4              ── E: 0     | W: 0     | N: 0                                                                                                              
✔ dynutils 1.0.11                        ── E: 0     | W: 0     | N: 0                                                                                                              
✔ applicable 0.1.0                       ── E: 1     | W: 0     | N: 0                                                                                                              
✔ LSX 1.4.0                              ── E: 0     | W: 0     | N: 1                                                                                                              
✔ seededlda 1.1.0                        ── E: 0     | W: 0     | N: 4                                                                                                              
✔ simona 1.0.10                          ── E: 0     | W: 1     | N: 2                                                                                                              
✔ scClassify 1.14.0                      ── E: 0     | W: 0     | N: 0                                                                                                              
✔ immcp 1.0.3                            ── E: 0     | W: 0     | N: 0                                                                                                              
✔ SimBu 1.4.3                            ── E: 0     | W: 0     | N: 2                                                                                                              
✔ simplifyEnrichment 1.12.0              ── E: 0     | W: 0     | N: 1                                                                                                              
✔ scMerge 1.18.0                         ── E: 2     | W: 0     | N: 0                                                                                                              
✔ scFeatures 1.3.2                       ── E: 0     | W: 1     | N: 2                                                                                                              
OK: 12                                                                                                                                                                            
BROKEN: 0
Total time: 1 hour
── REPORT ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Writing summary to 'revdep/README.md'
Writing problems to 'revdep/problems.md'
Writing failures to 'revdep/failures.md'
Writing CRAN report to 'revdep/cran.md'

[rcannood]

LGTM!

[koheiw]

I will submit to CRAN. Thanks.