[Rd] R 4.0.1-4.0.5 built with Intel Composer 19.0-19.1.1, errors in "make check" on CentOS 7.7-7.9

[Ryan Novosielski]

> On Apr 16, 2021, at 2:32 PM, Ivan Krylov <krylov.r00t using gmail.com> wrote:
> 
> On Fri, 16 Apr 2021 18:06:51 +0000
> Ryan Novosielski <novosirj using rutgers.edu> wrote:
> 
>> Well it definitely somehow could have, since it did
> 
> Wow! This is strange, but at least it should be easy to fix. Try editing
> the config.site file in the root of the R source directory and setting
> R_C_STACK_DIRECTION=down there. (Make sure to uncomment the line!)
> Re-run .../configure, make sure that src/include/config.h contains
> #define C_STACK_DIRECTION 1 and build R again.
> 
> Does the crash go away?

So, it does, and no other crashes, though the checks fail in a couple of places, and the final status is error: in tests/reg-tests-1d.R, and also reg-packages.R (those are the only two that have .Rout.fail files). 

make[3]: Entering directory `/scratch/novosirj/install-files/R-4.0.5-intel-19.1-build/tests'
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/array-subset.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-1a.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-1b.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-1c.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-1d.R' ...make[3]: *** [reg-tests-1d.Rout] Error 1
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to '/scratch/novosirj/install-files/R-4.0.5/tests/reg-tests-2.Rout.save' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-examples1.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-examples2.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/p-qbeta-strict-tst.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/r-strict-tst.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to '/scratch/novosirj/install-files/R-4.0.5/tests/reg-IO.Rout.save' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to '/scratch/novosirj/install-files/R-4.0.5/tests/reg-IO2.Rout.save' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to '/scratch/novosirj/install-files/R-4.0.5/tests/reg-plot.pdf.save' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-S4-examples.R' ... OK
running code in '/scratch/novosirj/install-files/R-4.0.5/tests/reg-BLAS.R' ... OK
make[3]: Leaving directory `/scratch/novosirj/install-files/R-4.0.5-intel-19.1-build/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/scratch/novosirj/install-files/R-4.0.5-intel-19.1-build/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Target `check' not remade because of errors.
make[1]: Leaving directory `/scratch/novosirj/install-files/R-4.0.5-intel-19.1-build/tests'
make: *** [check] Error 2

I’m a little new to reading these results, so I’m not sure exactly what I’m looking for. I’ve shared them in the event that what I put in this e-mail is useless:

reg-tests-1d.Rout.fail: https://rutgersconnect-my.sharepoint.com/:u:/g/personal/novosirj_oarc_rutgers_edu/EYK2JHWQ1-9Dvu6gK9lrkRIBkEyA4QqkeH7C4gmbAYyBBQ?e=lfGJL7
reg-packages.Rout.fail: https://rutgersconnect-my.sharepoint.com/:u:/g/personal/novosirj_oarc_rutgers_edu/EazCjI6fRnNKhQASFPeySBUBENVpCqCljFg3-sokBZJnAw?e=8lwywe

Anyhow, there appear to be a number of places, if I have this right:

[novosirj using amarel-test2 tests]$ grep -i -B2 ^error reg-packages.Rout.fail
building package exSexpr ...
Converting Rd files to LaTeX 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in running tools::texi2pdf()
--
Hmm ... looks like a package
Creating pdf output from LaTeX ...
Error: R CMD build failed (no tarball) for package exSexpr

These maybe seem like they’re OK, and if I don’t have pdf2latex, they’re expected? Unless I should be looking for something else other than “^Error”. That seemed like the only place something could be going wrong.

For the regression tests, these seem like some of them are actual problems, but maybe someone here knows if some are expected?

[novosirj using amarel-test2 R-4.0.5-intel-19.1-build]$ grep -i -B2 "Asserted error" tests/reg-tests-1d.Rout.fail 
> op <- options(device=function(...){}) # non-sense device
> tools::assertError(plot.new(), verbose = TRUE)
Asserted error: no active device and default getOption("device") is invalid
> if(no.grid <- !("grid" %in% loadedNamespaces())) requireNamespace("grid")
> tools::assertError(grid::grid.newpage(), verbose = TRUE)
Asserted error: no active device and default getOption("device") is invalid
--
> aKnots <- c(rep(0, 4), c(0.3, 0.5, 0.6), rep(1, 4))
> tools::assertError(splines::splineDesign(aKnots, x, derivs = 4), verbose = TRUE)
Asserted error: derivs = 4 >= ord = 4, but should be in {0,..,ord-1}
--
> ## Failed to work after r76382--8:
> tools::assertError(formula("3"), verbose=TRUE)
Asserted error: invalid formula "3": not a call
--
> noC <- structure(datasets::trees, class = c("noCol", "data.frame"))
> tools::assertError( noC[1,2], verbose=TRUE) # fails indeed
Asserted error:  [!] Column subscripts not allowed
--
> t2 <- lapply(Alis, head, 2)
> tools::assertError( head(Alis[[1]], c(1, NA)), verbose=TRUE)
Asserted error: invalid 'n' - length(n) must be <= length(dim(x)), got 2 > 1
> tools::assertError( tail(1:5, c(1, NA)), verbose=TRUE)
Asserted error: invalid 'n' - must have length one when dim(x) is NULL, got 2
--
> Foolis <- lapply(Alis, `class<-`, "foo")
> tools::assertError( head(Foolis[[1]], c(1, NA)), verbose=TRUE)
Asserted error: invalid 'n' - length(n) must be <= length(dim(x)), got 2 > 1
--
> tools::assertError(cbind(ts(1:2, start = 0.5, end = 1.5),
+                        ts(1:2, start = 0  , end = 1)), verbose=TRUE)
Asserted error: not all series have the same phase
--
> ## stopifnot() custom message now via <named> args:
> e <- tools::assertError(stopifnot("ehmm, you must be kidding!" = 1 == 0), verbose=TRUE)
Asserted error: ehmm, you must be kidding!
--
> e2 <- tools::assertError(
+  stopifnot("2 is not approximately 2.1" = all.equal(2, 2.1)), verbose=TRUE)
Asserted error: 2 is not approximately 2.1

Thanks again for your help!

--
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