Run Valgrind

[brodieG]

There are gremlins lurking, including issue #36, and:

> unitize_dir()

Prepping Unitizers...                                                           
 *** caught bus error ***
address 0x7fd3cd81ad78, cause 'non-existent physical address'

Traceback:
 1: initialize(value, ...)
 2: initialize(value, ...)
 3: new("unitizerBrowseSubSectionFailed", show.out = TRUE, show.msg = TRUE,     items.new = x@items.new[x@tests.fail & sect.map], show.fail = x@tests.errorDetails[x@tests.fail &         sect.map], items.ref = x@items.ref[x@items.new.map[x@tests.fail &         sect.map]], new.conditions = x@tests.conditions.new[x@tests.fail &         sect.map], tests.result = x@tests.result[x@tests.fail &         sect.map, , drop = FALSE])
 4: .local(x, mode, ...)
 5: (function (x, mode, ...) standardGeneric("browsePrep"))(dots[[1L]][[10L]], mode = dots[[2L]][[1L]],     start.at.browser = dots[[3L]][[10L]], hist.con = 3L, interactive = TRUE)
 6: (function (x, mode, ...) standardGeneric("browsePrep"))(dots[[1L]][[10L]], mode = dots[[2L]][[1L]],     start.at.browser = dots[[3L]][[10L]], hist.con = 3L, interactive = TRUE)
 7: mapply(browsePrep, as.list(unitizers), mode = mode, start.at.browser = (identical(mode,     "review") | !to.review) & !force.update, MoreArgs = list(hist.con = hist.obj$con,     interactive = interactive.mode), SIMPLIFY = FALSE)
 8: unitize_browse(unitizers = unitizers[valid], mode = mode, interactive.mode = interactive.mode,     force.update = force.update, auto.accept = auto.accept, history = history,     global = global)
 9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestarts(unitizers[valid] <- unitize_browse(unitizers = unitizers[valid],     mode = mode, interactive.mode = interactive.mode, force.update = force.update,     auto.accept = auto.accept, history = history, global = global),     unitizerInteractiveFail = function(e) interactive.fail <<- TRUE)
12: unitize_core(test.files = test.files, store.ids = store.ids,     state = state, pre = pre, post = post, history = history,     interactive.mode = interactive.mode, force.update = force.update,     auto.accept = auto.accept, mode = "unitize")
13: unitize_dir()

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n

But difficult to reproduce.

[brodieG]

Another:

> unitize_dir()

11/12 validate.args.R: fun5(1:2, NULL)                                          
 *** caught segfault ***
address 0xb, cause 'memory not mapped'

Traceback:
 1: `slot<-`(.Object, slotName, check = FALSE, slotVal)
 2: initialize(value, ...)
 3: initialize(value, ...)
 4: new("unitizerItemTestError", .new = item.new.dat, .ref = item.ref.dat)
 5: testItem(e1, e2)
 6: testItem(e1, e2)
 7: e1 + item
 8: e1 + item
 9: unitizer + tests
10: unitizer + tests
11: unitize_eval(tests.parsed = tests.parsed[valid], unitizers = unitizers[valid],     global = global)
12: unitize_core(test.files = test.files, store.ids = store.ids,     state = state, pre = pre, post = post, history = history,     interactive.mode = interactive.mode, force.update = force.update,     auto.accept = auto.accept, mode = "unitize")
13: unitize_dir()

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n

[brodieG]

See also https://github.com/joshuaulrich/rchk-docker

[brodieG]

We're going to close this issue for now even though we're not getting perfectly clean valgrind runs. With R -d 'valgrind --dsymutil=yes --tool=memcheck', we're seeing with:

  vet(
    !anyNA(.),
    c(234234131431, 123413413413, 1341341341, 12341234134, 562456234, 24624624,
      2452345234, 2345234524, 23452452, 2243524352, 254254234, 2452452435, NA)
  )

==45756== Invalid read of size 16
==45756==    at 0x1017D7625: _platform_memchr$VARIANT$Base (in /usr/lib/system/libsystem_platform.dylib)
==45756==    by 0x111B1A78F: CSR_strmcpy (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x111B234C6: VALC_process_error (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x111B237B7: VALC_validate (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x10011ADD4: R_doDotCall (dotcode.c:0)
==45756==    by 0x10011C6B2: do_dotcall (dotcode.c:1252)
==45756==    by 0x10014AB3C: Rf_eval (eval.c:728)
==45756==    by 0x10015AE51: R_execClosure (eval.c:1607)
==45756==    by 0x10014A9E9: Rf_eval (eval.c:747)
==45756==    by 0x10018AF47: Rf_ReplIteration (main.c:258)
==45756==    by 0x10018C43E: run_Rmainloop (main.c:308)
==45756==    by 0x100000F5A: main (in /Library/Frameworks/R.framework/Resources/bin/exec/R)
==45756==  Address 0x1030d5150 is 8 bytes after a block of size 232 alloc'd
==45756==    at 0x100094671: malloc (in /usr/local/Cellar/valgrind/HEAD-16457/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
==45756==    by 0x10019556D: Rf_allocVector3 (memory.c:2672)
==45756==    by 0x100142BC3: Rf_mkCharLenCE (envir.c:3884)
==45756==    by 0x100184AC1: Rf_mkString (Rinlinedfuns.h:697)
==45756==    by 0x111B1BE8D: VALC_evaluate_recurse (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x111B1C066: VALC_evaluate (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x111B23695: VALC_validate (in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/vetr/libs/vetr.so)
==45756==    by 0x10011ADD4: R_doDotCall (dotcode.c:0)
==45756==    by 0x10011C6B2: do_dotcall (dotcode.c:1252)
==45756==    by 0x10014AB3C: Rf_eval (eval.c:728)
==45756==    by 0x10015AE51: R_execClosure (eval.c:1607)
==45756==    by 0x10014A9E9: Rf_eval (eval.c:747)
==45756== 

The best conclusion I could come up with on debugging is that the error is actually coming from CSR_strmlen_x, and in particular, from the use of memchr therein, where memchr is reading memory in blocks and as such overshoots the '\0'. Note the _platform_memchr$VARIANT$Base.