Error in dim(sssf)

Interfaces RStan
1

Hi,

I am dealing with an error message that I do not fully understand and I am also unable to get my model to work.

Whenever I run a Stan model in R with thin=5 I get this error message:
Error in dim(sssf) <- c(n2, object@sim$chains, length(tidx)) :
dims [product 0] do not match the length of object [2584]

I assume the error comes from code line 481 here: https://github.com/cran/rstan/blob/master/R/stanfit-class.R

When I set thin=1 I end up with this error:
Error in FUN(newX[, i], …) : is.atomic(x) is not TRUE

Both error appear after the all chains have ran.

But I do not understand how I caused this error and also not how to fix it.

I updated all packages and the error persists.

Best,
Lucas

  • Operating System: Mac OSX Catalina
  • RStan Version: 2.19.2
  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
    CXXFLAGS=-O3 -mtune=native -march=native
    CXXFLAGS= -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined

CC=clang
CXX=clang++ -arch x86_64 -ftemplate-depth-256

CXXFLAGS=-O3 -mtune=native -march=native
CXXFLAGS= -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined

CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256

  • Output of devtools::session_info("rstan")

─ Session info ───────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os macOS Catalina 10.15.1
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2019-12-07

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
BH 1.69.0-1 2019-01-07 [1] CRAN (R 3.6.0)
callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
checkmate 1.9.4 2019-07-04 [1] CRAN (R 3.6.0)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
farver 2.0.1 2019-11-13 [1] CRAN (R 3.6.0)
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.6.0)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.0)
loo 2.1.0 2019-03-13 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
MASS * 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.0)
matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.0)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
nlme 3.1-142 2019-11-07 [1] CRAN (R 3.6.0)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp * 1.0.3 2019-11-08 [1] CRAN (R 3.6.0)
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 3.6.0)
reshape2 * 1.4.3 2017-12-11 [1] CRAN (R 3.6.0)
rlang 0.4.2 2019-11-23 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rstan * 2.19.2 2019-07-09 [1] CRAN (R 3.6.0)
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0)
StanHeaders * 2.19.0 2019-09-07 [1] CRAN (R 3.6.0)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.0)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

2

I would leave thin at 1. When you get an error from that, what is the output of

traceback()

?

3

Thank you very much for responding.

For “thin=1” it is:

traceback()
9: stop(simpleError(msg, call = if (p ← sys.parent(1L)) sys.call(p)))
8: stopifnot(is.atomic(x))
7: FUN(newX[, i], …)
6: apply(E, 2, var)
5: throw_sampler_warnings(nfits)
4: .local(object, …)
3: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,
check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,
verbose = verbose, algorithm = match.arg(algorithm), control = control,
check_unknown_args = FALSE, cores = cores, open_progress = open_progress,
include = include, …)
2: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,
check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,
verbose = verbose, algorithm = match.arg(algorithm), control = control,
check_unknown_args = FALSE, cores = cores, open_progress = open_progress,
include = include, …)
1: stan(file = “Lucas Playground/Code/Stan2d.stan”, data = CH_data,
iter = 1000, warmup = 1000, chains = 4, thin = 1, init = “random”,
verbose = TRUE, cores = 4, seed = 4321, save_warmup = TRUE)

For “thin=5”

I get these warning messages:
Registered S3 method overwritten by ‘xts’:
method from
as.zoo.xts zoo

and this is the traceback output:

traceback()
10: .local(object, …)
9: extract(x, permuted = FALSE, inc_warmup = FALSE, …)
8: extract(x, permuted = FALSE, inc_warmup = FALSE, …)
7: as.array.stanfit(object)
6: as.array(object)
5: throw_sampler_warnings(nfits)
4: .local(object, …)
3: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,
check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,
verbose = verbose, algorithm = match.arg(algorithm), control = control,
check_unknown_args = FALSE, cores = cores, open_progress = open_progress,
include = include, …)
2: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,
check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,
verbose = verbose, algorithm = match.arg(algorithm), control = control,
check_unknown_args = FALSE, cores = cores, open_progress = open_progress,
include = include, …)
1: stan(file = “Lucas Playground/Code/Stan2d.stan”, data = CH_data,
iter = 1000, warmup = 1000, chains = 4, thin = 5, init = “random”,
verbose = TRUE, cores = 4, seed = 4321, save_warmup = TRUE)

Best wishes,
Lucas

4

You set warmup=1000 and iter=1000, but what you probably mean is iter=2000, because iter is the total number of iterations including warmup. This will produce a better error in the next version (https://github.com/stan-dev/rstan/issues/693).

Perhaps there’s a strange interaction with thin which could be a different bug.

5

That is it - thank you!

6

I was bit by the same error now after a computation that took a couple of hours, which was frustrating. I think the issue was that the numbers for iterations, warmup, and thinning were not consistent / divisible / integers (my mistake). It would be useful to add a check in rstan/stan itself to check that this will not happen before it starts sampling, as it can be easily computed before and can save some hours of estimation in case of user error.