macOS support + update code to fetch and build llvm

[Jakobeha]

• specifically looking at macOS ARM, with homebrew (where library code is in /opt/homebrew)

R_ENABLE_JIT=0 works

PIR_DEBUG=PrintEarlyPir,PrintFinalPir,... seem to create more issues
PIR_DEBUG=DryRun hasn't produced issues so far though some of the tests take a really long time, so they might be hanging

Here are log snippets of some of the test failures:

> for (i in 1:10) {
+     f12()
+ }

 *** caught segfault ***
address 0x100000020, cause 'invalid permissions'

Traceback:
 1: make.names(vnames, unique = TRUE)
 2: data.frame(x = ts(c(41, 42, 43)), y = c(61, 62, 63))
 3: f12()
An irrecoverable exception occurred. R is aborting now ...
*************************************************************************************
***  end log pir_regression2.R
*************************************************************************************
*

> dyn.load('/Users/jakobeha/Documents/grad/research/rir/build/librir.dylib')
> source('/Users/jakobeha/Documents/grad/research/rir/tools/../rir/R/rir.R')
> library(Matrix)
Error: package or namespace load failed for ‘Matrix’ in loadNamespace(package, lib.loc):
 bad target context--should NEVER happen if R was called correctly
Execution halted
*************************************************************************************
***  end log regression_spModel.matrix.R
*************************************************************************************
*************************************************************************************
xargs: bash: exited with status 255; aborting

> utils::str(allinfoNS("stats"))
List of 9
 $ DLLs          :List of 1
  ..$ stats:List of 5
  .. ..$ name         : chr "stats"
  .. ..$ path         : chr "/Users/jakobeha/Documents/grad/research/rir/external/custom-r/library/stats/libs/stats.so"
  .. ..$ dynamicLookup: logi FALSE
  .. ..$ handle       :
 *** caught segfault ***
address 0x10, cause 'invalid permissions'

Traceback:
 1: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
 2: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev +     1, indent.str = paste(indent.str, ".."))
 3: str.default(obj, ...)
 4: str(obj, ...)
 5: (function (...) str(obj, ...))(max.level = base::quote(NA), vec.len = base::quote(4L),     digits.d = base::quote(3L), nchar.max = base::quote(128),     give.attr = base::quote(TRUE), drop.deparse.attr = base::quote(TRUE),     give.head = base::quote(TRUE), width = base::quote(80L),     envir = base::quote(NULL), strict.width = base::quote("no"),     formatNum = base::quote(function (x, ...)     format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = base::quote(99L),     deparse.lines = base::quote(NULL), give.length = base::quote(TRUE),     nest.lev = base::quote(2), indent.str = base::quote("  .. .."))
 6: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
 7: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev +     1, indent.str = paste(indent.str, ".."))
 8: str.default(obj, ...)
 9: str(obj, ...)
10: (function (...) str(obj, ...))(max.level = base::quote(NA), vec.len = base::quote(4L),     digits.d = base::quote(3L), nchar.max = base::quote(128),     give.attr = base::quote(TRUE), drop.deparse.attr = base::quote(TRUE),     give.head = base::quote(TRUE), width = base::quote(80L),     envir = base::quote(NULL), strict.width = base::quote("no"),     formatNum = base::quote(function (x, ...)     format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = base::quote(99L),     deparse.lines = base::quote(NULL), give.length = base::quote(TRUE),     nest.lev = base::quote(1), indent.str = base::quote("  .."))
11: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
12: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev +     1, indent.str = paste(indent.str, ".."))
13: str.default(allinfoNS("stats"))
14: utils::str(allinfoNS("stats"))
An irrecoverable exception occurred. R is aborting now ...
*************************************************************************************
***  end log pir_regression6.R
*************************************************************************************
*************************************************************************************
xargs: bash: exited with status 255; aborting

> dyn.load('/Users/jakobeha/Documents/grad/research/rir/build/librir.dylib')
> source('/Users/jakobeha/Documents/grad/research/rir/tools/../rir/R/rir.R')
>   a <- b <- 0
>   plot(a, b    
+        )
> example(glm )
Error in loadNamespace(x) : 
  bad target context--should NEVER happen if R was called correctly
Calls: example -> loadNamespace
Execution halted
*************************************************************************************
***  end log regression_stats.R
*************************************************************************************
*************************************************************************************
xargs: bash: exited with status 255; aborting

> mkDend <- function(n, lab, method = "complete",
+                    ## gives *ties* often:
+                  rGen = function(n) 1+round(16*abs(rnorm(n)))) {
+     stopifnot(is.numeric(n), length(n) == 1, n >= 1, is.character(lab))
+     a <- matrix(rGen(n*n), n, n)
+     colnames(a) <- rownames(a) <- paste0(lab, 1:n)
+     .HC. <<- hclust(as.dist(a + t(a)), method=method)
+     as.dendrogram(.HC.)
+ }
> 
> ## recursive dendrogram methods and deeply nested dendrograms
> op <- options(expressions = 999)# , verbose = 2) # -> max. depth= 961
> set.seed(11); d <- mkDend(1500, "A", method="single")
> rd <- reorder(d, nobs(d):1)

 *** caught segfault ***
address 0x1, cause 'invalid permissions'

Traceback:
 1: match.arg(method)
 2: order(x, na.last = na.last, decreasing = decreasing, method = "radix")
 3: sort.list(vals)
 4: oV(x, wts)
 5: stopifnot(inherits(x, "dendrogram"))
 6: midcache.dendrogram(oV(x, wts))
 7: reorder.dendrogram(d, nobs(d):1)
 8: reorder(d, nobs(d):1)
An irrecoverable exception occurred. R is aborting now ...
*************************************************************************************
***  end log reg-tests-1c.R
*************************************************************************************
*************************************************************************************
xargs: bash: exited with status 255; aborting

#1193

[o-]

Here are some stats for your PR:

• WARNING: the longest CI job test_release_2 took 2.41h
• are-we-fast-r suite regressed by 0.96
• Bounce_nonames_simple regressed by 0.94
• fasta_naive regressed by 0.91
• emptyFor regressed by 0.83
• Overall benchmarks regressed by 1.0

Please find your performance results at https://rir-benchmarks.prl.fit.cvut.cz/diff?job_ids[]=4369453822&job_ids[]=4371607270&selection=all