escape one frollsd tests for valgrind #7548

jangorecki · 2025-12-29T19:00:17Z

Haven't tested, but looking at

Fri Dec 26 02:23:49 2025 endian==little, sizeof(long double)==16, capabilities('long.double')==TRUE, longdouble.digits==53, sizeof(pointer)==8, TZ==unset,

and

exact_NaN = isTRUE(capabilities()["long.double"]) && identical(as.integer(.Machine$longdouble.digits), 64L)

I think it should do

MichaelChirico · 2025-12-29T19:03:31Z

inst/tests/froll.Rraw

 exact_NaN = isTRUE(capabilities()["long.double"]) && identical(as.integer(.Machine$longdouble.digits), 64L)
 if (!exact_NaN) {
-  cat("\n**** Skipping 7 NaN/NA algo='exact' tests because .Machine$longdouble.digits==", .Machine$longdouble.digits, " (!=64); e.g. under valgrind\n\n", sep="")
+  cat("\n**** Skipping 8 NaN/NA algo='exact' tests because .Machine$longdouble.digits==", .Machine$longdouble.digits, " (!=64); e.g. under valgrind\n\n", sep="")


Maybe we could do something like nskip for foreign messages to avoid incrementing this manually

data.table/R/test.data.table.R

Line 336 in 7e9907f

if (foreign && nskip > 0L) catf("Skipped %d tests for translated messages. ", nskip) # nocov

codecov · 2025-12-29T19:08:05Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.96%. Comparing base (291a711) to head (c524ccf).
⚠️ Report is 5 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #7548      +/-   ##
==========================================
- Coverage   98.97%   98.96%   -0.02%     
==========================================
  Files          87       87              
  Lines       16733    16737       +4     
==========================================
+ Hits        16561    16563       +2     
- Misses        172      174       +2

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MichaelChirico · 2025-12-29T19:17:44Z

inst/tests/froll.Rraw

 y = c(1e8+2.980232e-8, 1e8, 1e8, 1e8) # CLAMP0 test
 test(6001.731, frollvar(y, 3)[4L], 0)
-test(6001.732, frollsd(y, 3)[4L], 0)
+if (exact_NaN) test(6001.732, frollsd(y, 3)[4L], 0)


the other cases are all using algo='exact', so this would be the first case being skipped with algo='fast'

it's also v. interesting that frollvar(y, 3)[4L], which per glancing the implementation only differs by applying sqrt(), does not have this numerical difference issue

Yes, sqrt must be causing this rounding error

We could possibly use all.equal here instead... Then no need to escape test

Any idea why 2.980232e-8 was chosen? Maybe we could make that a function of .Machine$double.eps (assuming that changes on/off valgrind) or of .Machine$longdouble.digits?

Looks like the CLAMP0 in the comment refers to something that was refactored...

#7361 (comment)

c2c5bde#diff-6eb444de657f71e8b89b3d686c4ec70e4ecff4e33154481d0b1b416d09449f1eL1140

Seems @ben-schwen came up with that number:

#7361 (comment)

2.980232e-8 was chosen because without clamp, it produced wrong results. AFAIR I used rnorm with e-16 or smth and pushed onto frollsd until I found the example (with 3 or 4 other candidates) because the code looked numerically unstable (hitting negative numbers).

Thanks for the extra context, very helpful. I did a similar exercise (with rnorm(1e6, sd=1e-8) to be precise) and found that, absent the clamping added in #7361, we can trigger the negative result on valgrind with a different epsilon:

y = c(1e8-0.000000017353503836151923775668, 1e8, 1e8, 1e8) frollvar(y, 3) # [1] NA NA 0.000000e+00 -1.110223e-16

But it does seem prohibitively difficult to come up with an epsilon that fails with and without valgrind, and I'm not sure there's anything but cleverness points to score there anyway.

We could possibly use all.equal here instead... Then no need to escape test

wound up doing essentially this, but all.equal() won't do because the intent of the test is to ensure the result is strictly non-negative.

* escape one tests for valgrind * increment skipped count * escape proper one * make test robust to valgrind numerical issues --------- Co-authored-by: Michael Chirico <[email protected]>

@manmita

* 1.18.0 on CRAN. Bump to 1.18.99 * bump versions * Fix milestone link for 1.18.2 * Replace `ATTRIB`, `SET_ATTRIB` (#7487) * frev: drop SET_ATTRIB Instead, backport and use CLEAR_ATTRIB (R >= 4.5). * mergeIndexAttrib: drop SET_ATTRIB Use SHALLOW_DUPLICATE_ATTRIB (R >= 3.3) for the simple case. Also, Backport ANY_ATTRIB (R >= 4.5) instead of testing !isNull(ATTRIB(.)). * cbindlist: use ANY_ATTRIB * nafillR: use ANY_ATTRIB * Backport R_mapAttrib * anySpecialStatic: switch to R_mapAttrib * dogroups: construct rownames anew Instead of trying to walk ATTRIB in search of the compact 'rownames' attribute to modify, install it anew, take note of the returned reference to the value being installed (a different one!) and modify that. * mergeIndexAttrib: switch to R_mapAttrib * assign: factor out index fixup Instead of walking the attribute list directly, use R_mapAttrib(). Create a hash table of index names instead of relying on chin() and a temporary string vector. Move all temporary allocations onto the R heap. * assign: drop indexLength * assign: fix index unmarking * Comments, better field names * Update src/dogroups.c Co-authored-by: Benjamin Schwendinger <[email protected]> * mapAttrib: protect the attribute value Otherwise the callback could remove the attribute and end up with the value unprotected. Protect the attribute tag as well for uniformity. Co-Authored-By: HughParsonage <[email protected]> * dogroups: look up rownames using mapAttrib This solution is closer to the working approach previously taken by the code. * Fix comment, function name * Protect the newly found rownames attribute * add NEWS entry --------- Co-authored-by: HughParsonage <[email protected]> Co-authored-by: Benjamin Schwendinger <[email protected]> Co-authored-by: Michael Chirico <[email protected]> Co-authored-by: Michael Chirico <[email protected]> * use getVar over findVar (#7575) * remove unused vars (#7578) * Fix code blocks in NEWS.md (#7518) Add a missing triple-backtick separator. Separate the indented code blocks from the preceding paragraph because otherwise Pandoc fails to realise that the whitespace followed by triple-backtick denotes a fenced code block. * make rchk happy (#7520) Co-authored-by: Michael Chirico <[email protected]> * escape one frollsd tests for valgrind (#7548) * escape one tests for valgrind * increment skipped count * escape proper one * make test robust to valgrind numerical issues --------- Co-authored-by: Michael Chirico <[email protected]> * fix(7571): bug fix for narm issue on gforce in int64 case (#7572) * fix(7571): bug fix for narm issue on gforce in int64 case * fix(7571): test sequencing * fix(7571): updated the NEWS.md * trailing newline * Use $V1 * fix(7571): added db optimize 2L * refine NEWS * fix(7571): add more tests and change to code similar to int for gsum * fix(7571): added more tests for mean * eliminate intermediate variable * NEWS again --------- Co-authored-by: Michael Chirico <[email protected]> * add @manmita (#7573) * `utils.c`: include `<signal.h>` for `siginfo_t` (#7517) * utils.c: include <signal.h> for siginfo_t POSIX says: > The <signal.h> header shall define the siginfo_t type as a structure So <sys/wait.h> is not enough to see the definition (not just a forward declaration) of siginfo_t. * NEWS entry * Amend NEWS * more robustly define _POSIX_C_SOURCE (h/t Hugh) * tidy up NEWS * -D_POSIX_C_SOURCE=200809L in gitlab CI job for regression test * revert gitlab-ci change --------- Co-authored-by: Michael Chirico <[email protected]> Co-authored-by: Michael Chirico <[email protected]> * Remove unrelated release notes Amend 1c05f11: remove the notes not relevant to the 1.18.2 release. * Fix http -> https link that is now a redirect (#7588) Found the following (possibly) invalid URLs: URL: http://stereopsis.com/radix.html (moved to https://stereopsis.com/radix.html) From: man/setkey.Rd man/setorder.Rd Status: 200 Message: OK * Fix latest rchk issues (#7585) * attempt PROTECT for new rchk issues * different approach for longestLevels * use nprotect? * no longer using names SEXP * only UNPROTECT near exit * no, that cant be it... * move assignment into loop * REPROTECT approach * reduce diff * reduce diff * set automatically allocates new column slots if needed (#7538) * set automatically allocates new column slots if needed * use GetOption1 instead of GetOption * fix test * change froll test * remove assign change * add output statements to test loop * add helper function * frollmedianFast: avoid reading uninitialised array (#7589) The 'n' array is only initialised if 'even' is true, so skip the comparisons otherwise. Detected by checking with --use-valgrind or performing a frollmedian() with an odd window size under R -d valgrind. Fixes: #7546 * `setlevels()`: avoid crash on missing factor values (#7596) Check for missing or out of bounds values and set them to NA. * Avoid out-of-bounds access in `overlaps` (#7598) * Add tests * overlaps: avoid accessing length-0 vectors in ux If 'ux' contains 0 rows, pretend that all comparisons against its non-existent elements fail. * overlaps: avoid 'lookup' list overflow This used to happen when from[i] was 0. (No match on non-range columns?) * NEWS entry * overlaps: uncomment one more underflow test Technically this one was harmless (and thus not caught by sanitizers) because the preceding VECSEXP header always contained a 0, preventing the branch where VECTOR_ELT() would be called with a negative index. * test formatting * Update src/ijoin.c Co-authored-by: Benjamin Schwendinger <[email protected]> * Update src/ijoin.c Co-authored-by: Benjamin Schwendinger <[email protected]> * Update src/ijoin.c Co-authored-by: Benjamin Schwendinger <[email protected]> * Update inst/tests/tests.Rraw * overlaps: uncomment the remaining underflow test The underflow is covered by already existing tests. --------- Co-authored-by: Benjamin Schwendinger <[email protected]> * Only export R_init_data_table (#7607) This will avoid name clashes between data.table functions (now hidden) and other functions in the global namespace visible to the shared library loader. Fixes: #7605 * `set()`: only reallocate the table if resizing would fail otherwise (#7606) * Regression tests * set(): only reallocate if resizing would fail * Update R/data.table.R Co-authored-by: Michael Chirico <[email protected]> * Rename test variables Co-Authored-By: Michael Chirico <[email protected]> * Cache j %chin% names(x) Co-Authored-By: Benjamin Schwendinger <[email protected] --------- Co-authored-by: Michael Chirico <[email protected]> Co-authored-by: Michael Chirico <[email protected]> * NEWS entry for #7607 (#7608) * NEWS entry for #7607 * More about the problem being solved Co-Authored-By: Benjamin Schwendinger <[email protected]> * `tests/froll.R`: disable `mcparallel` under Valgrind (#7621) * update NEWS * fix merge --------- Co-authored-by: Tyson Barrett <[email protected]> Co-authored-by: aitap <[email protected]> Co-authored-by: HughParsonage <[email protected]> Co-authored-by: Michael Chirico <[email protected]> Co-authored-by: Michael Chirico <[email protected]> Co-authored-by: Jan Gorecki <[email protected]> Co-authored-by: Manmita Das <[email protected]>

jangorecki added 2 commits December 29, 2025 19:58

escape one tests for valgrind

30f2a4f

increment skipped count

9b91c2c

jangorecki requested a review from MichaelChirico as a code owner December 29, 2025 19:00

escape proper one

5d50ca9

MichaelChirico reviewed Dec 29, 2025

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aitap mentioned this pull request Dec 29, 2025

valgrind issue in 1.18.0 #7546

Closed

make test robust to valgrind numerical issues

c524ccf

MichaelChirico approved these changes Dec 31, 2025

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Merge branch 'master' into frollsd-non-exact

e546f30

MichaelChirico merged commit 7d70b15 into master Jan 2, 2026
9 checks passed

MichaelChirico deleted the frollsd-non-exact branch January 2, 2026 21:14

MichaelChirico added this to the 1.18.2 milestone Jan 14, 2026

aitap mentioned this pull request Jan 24, 2026

Fix CRAN R CMD check issues by 2026-02-01 #7587

Closed

escape one frollsd tests for valgrind #7548

escape one frollsd tests for valgrind #7548

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