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[R-pkg-devel] Cannot reproduce CRAN error (Solaris i386)

3 messages · Daeyoung Lim, Gábor Csárdi

Daeyoung Lim
# 
Hello,

I have a package on CRAN called 'metapack' and received a message from
Professor Ripley that the error must be resolved for the package to be
safely retained in CRAN. I've encountered this error on R-CMD-check on
GitHub but cannot replicate it on any of my local machines to save my life.
The reproducible code snippet is as follows (I use Rcpp/RcppArmadillo):

library(metapack)
data("cholesterol")
Outcome <- model.matrix(~ pldlc + phdlc + ptg, data = cholesterol)
SD <- model.matrix(~ sdldl + sdhdl + sdtg, data = cholesterol)
Trial <- cholesterol$Trial
Treat <- cholesterol$trt
Npt <- cholesterol$Npt
XCovariate <- model.matrix(~ 0 + bldlc + bhdlc + btg + age + durat +
white + male + dm, data = cholesterol)
WCovariate <- model.matrix(~ trt, data = cholesterol)

fmodel <- 1
set.seed(2797542)
fit <- bayes.parobs(Outcome, SD, XCovariate, WCovariate, Treat, Trial,
  Npt, fmodel, mcmc = list(ndiscard = 1, nskip = 1, nkeep = 1),
  scale_x = TRUE, group = cholesterol$onstat, verbose = FALSE)

which gives me the following error:

warning: chol(): given matrix is not symmetric  error: chol():
decomposition failed

This can't be true because (1) it runs without problem on other machines,
(2) every matrix that is Cholesky-decomposed is ensured to be symmetric
through Sig = 0.5 * (Sig + Sig.t());. Even with Sig = arma::symmatu(Sig)
doesn't seem to guarantee symmetry.

Has anyone encountered something similar to this?
Thank you for your time.

*Daeyoung Lim, MS*

Ph.D. Student

Department of Statistics

University of Connecticut

Philip E. Austin, <https://goo.gl/maps/HsS7bzAMgCw>215 Glenbrook Road
<https://goo.gl/maps/HsS7bzAMgCw>

Storrs Mansfield, CT 06269-4120 <https://goo.gl/maps/HsS7bzAMgCw>
Gábor Csárdi
# 
FWIW this code does not give me any warnings or errors on Solaris and
R 4.0.4 and the current CRAN version of metapack.

Gabor
On Thu, Feb 18, 2021 at 1:54 AM Daeyoung Lim <daeyoung.lim at uconn.edu> wrote:
Gábor Csárdi
# 
Actually, I can reproduce it if I use the Oracle Studio compilers. You
can also reproduce it on R-hub like this:

rhub::check("metapack_0.1.0.tar.gz", platform = "solaris-x86-patched-ods")

I suggest you fix the valgrind issues first, because they might be
causing this crash as well.

You can also get a Solaris VM, to make it easier to debug the issue on
Solaris: https://github.com/r-hub/solarischeck/tree/master/packer Let
me know if you don't want to build the VM yourself, and I can give you
access to one.

Gabor
On Thu, Feb 18, 2021 at 10:54 AM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: