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Warning - 'config' variable 'CPP' is deprecated
Summary:
After encountering #774 and installing this version of rstan I get a 'config' variable 'CPP' is deprecated warning message / error. I think this is happening here. It looks like this was depreciated in R 3.6.2: https://cran.r-project.org/bin/windows/base/old/3.6.2/NEWS.R-3.6.2.html
Everything Stan related still works as it should, but it makes some of my package's tests fail.
Reproducible Steps:
library(rstan)
res <- stan_model(
model_code = "data {} parameters {real x;} model {x ~ std_normal();}"
)
gives :
'config' variable 'CPP' is deprecated
clang -mmacosx-version-min=10.13 -E
Warning message:
In system(paste(CPP, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
error in running command
RStan Version:
‘2.21.3’, 27a744a
R Version:
"R version 4.0.3 (2020-10-10)"
Operating System:
OS X 10.15.7
clang info
$ clang --version
Apple clang version 12.0.0 (clang-1200.0.32.27)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Thanks for reporting this. If that's deprecated we should remove it. I don't really know anything about this so tagging @bgoodri in case he hasn't seen this yet.
As for the failing tests, @hhau do you know why this is causing a failure if Stan ends up running properly despite the warning? Are the tests set up to fail if there are any warnings at all? I thought tests should pass with warnings unless you use something like testthat::expect_silent(). Anyway, I'm just curious. We should definitely fix the problem regardless.
I thought tests should pass with warnings unless you use something like
testthat::expect_silent()
Yes, you are correct and this is what happens (Apologies, my earlier comment was wrong).
> devtools::test()
Loading wsre
Loading required package: wsre
Testing wsre
✔ | OK F W S | Context
✔ | 5 | evaluate function [1.1 s]
✔ | 3 | naive ratio estimate
✔ | 2 | povertygap model can be run without errors [19.9 s]
✔ | 4 | weighted ratio estimate [0.2 s]
⠙ | 2 | wsre method'config' variable 'CPP' is deprecated
clang -mmacosx-version-min=10.13 -E
✔ | 6 1 | wsre function [33.3 s]
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
test_wsre-main.R:58: warning: Passing in stanmodel, with correct data block, leads to wsre_obj
error in running command
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
Duration: 54.6 s
OK: 20
Failed: 0
Warnings: 1
Skipped: 0
Glad the tests aren't failing, but thanks for letting us know about this warning.
@bgoodri Just following up here to say that with the latest 2.21.3 from github I'm also seeing the same warning @hhau reported:
'config' variable 'CPP' is deprecated
clang -mmacosx-version-min=10.13 -E
and then
Warning messages:
1: In system(paste(CPP, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
error in running command
None of these prevent it from running but it would be good to clean them up for the next release.
Also experiencing this since updating to Big Sur 11.2 and R 4.0.3, rstan 2.21.3
Clang version:
$ clang --version
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin20.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
It is a relatively new R development. We'll deal with it.
On Sun, Feb 7, 2021 at 2:25 PM jpkrooney [email protected] wrote:
Also experiencing this since updating to Big Sur 11.2 and R 4.0.3, rstan 2.21.3
Clang version:
$ clang --version Apple clang version 12.0.0 (clang-1200.0.32.29) Target: x86_64-apple-darwin20.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin
[image: Screenshot 2021-02-07 at 20 21 07] https://user-images.githubusercontent.com/41968663/107157018-06761900-6982-11eb-8212-7cdf7f4dfbcc.png
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/862#issuecomment-774742122, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZ2XKUYN2KQAAKGM5LQNIDS53SI3ANCNFSM4SZYGNIQ .
After updating to the latest R version, this now works. But I'll keep the post here, in case someone else with the older R version is experiencing the same error.
I originally got both the "clang -mmacosx-version-min=10.13 -E" warning and the unserialize error, even with the most recent rstan version:
Compiling Stan program...
'config' variable 'CPP' is deprecated
clang -mmacosx-version-min=10.13 -E
Start sampling
starting worker pid=6764 on localhost:11209 at 13:37:42.657
starting worker pid=6778 on localhost:11209 at 13:37:42.928
starting worker pid=6792 on localhost:11209 at 13:37:43.197
starting worker pid=6806 on localhost:11209 at 13:37:43.471
SAMPLING FOR MODEL 'a379d9db763198ccb913a700062bad2e' NOW (CHAIN 1).
SAMPLING FOR MODEL 'a379d9db763198ccb913a700062bad2e' NOW (CHAIN 2).
SAMPLING FOR MODEL 'a379d9db763198ccb913a700062bad2e' NOW (CHAIN 3).
Error in unserialize(socklist[[n]]) : error reading from connection
In addition: Warning message:
In system(paste(CPP, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
error in running command
Called from: unserialize(socklist[[n]])
Even with:
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.5 (2021-03-31)
os macOS High Sierra 10.13.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Denver
date 2021-06-12
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2)
arrayhelpers 1.1-0 2020-02-04 [1] CRAN (R 4.0.2)
assertthat * 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.2)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2)
bayesplot 1.8.0 2021-01-10 [1] CRAN (R 4.0.2)
bayestestR 0.10.0 2021-05-31 [1] CRAN (R 4.0.2)
boot 1.3-28 2021-05-03 [1] CRAN (R 4.0.2)
bridgesampling 1.1-2 2021-04-16 [1] CRAN (R 4.0.2)
brms * 2.15.9 2021-06-12 [1] Github (paul-buerkner/brms@ffe2673)
Brobdingnag 1.2-6 2018-08-13 [1] CRAN (R 4.0.2)
broom * 0.7.6 2021-04-05 [1] CRAN (R 4.0.2)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.0.2)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.2)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2)
cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.2)
coda 0.19-4 2020-09-30 [1] CRAN (R 4.0.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.0.5)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.0.2)
colourpicker 1.1.0 2020-09-14 [1] CRAN (R 4.0.2)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.0.2)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
crosstalk 1.1.1 2021-01-12 [1] CRAN (R 4.0.2)
curl 4.3.1 2021-04-30 [1] CRAN (R 4.0.5)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.2)
dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.0.2)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.2)
devtools * 2.4.2 2021-06-07 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
distributional 0.2.2 2021-02-02 [1] CRAN (R 4.0.2)
dplyr * 1.0.6 2021-05-05 [1] CRAN (R 4.0.2)
DT 0.18 2021-04-14 [1] CRAN (R 4.0.2)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.5)
emmeans 1.6.1 2021-06-01 [1] CRAN (R 4.0.2)
estimability 1.3 2018-02-11 [1] CRAN (R 4.0.2)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.0.5)
farver 2.1.0 2021-02-28 [1] CRAN (R 4.0.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.2)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
gamm4 0.2-6 2020-04-03 [1] CRAN (R 4.0.2)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2)
ggdist 2.4.1 2021-06-10 [1] CRAN (R 4.0.5)
ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.2)
ggridges 0.5.3 2021-01-08 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
gtools 3.9.2 2021-06-06 [1] CRAN (R 4.0.2)
haven 2.4.1 2021-04-23 [1] CRAN (R 4.0.2)
hms 1.1.0 2021-05-17 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
htmlwidgets 1.5.3 2020-12-10 [1] CRAN (R 4.0.2)
httpuv 1.6.1 2021-05-07 [1] CRAN (R 4.0.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
igraph 1.2.6 2020-10-06 [1] CRAN (R 4.0.2)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.0.2)
insight 0.14.1 2021-05-28 [1] CRAN (R 4.0.5)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2)
later 1.2.0 2021-04-23 [1] CRAN (R 4.0.2)
lattice 0.20-44 2021-05-02 [1] CRAN (R 4.0.2)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
lme4 1.1-27 2021-05-15 [1] CRAN (R 4.0.2)
loo 2.4.1.9000 2021-06-11 [1] Github (stan-dev/loo@0117858)
lubridate 1.7.10 2021-02-26 [1] CRAN (R 4.0.2)
magrittr * 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.2)
MASS 7.3-54 2021-05-03 [1] CRAN (R 4.0.2)
Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.0.2)
matrixStats 0.59.0 2021-06-01 [1] CRAN (R 4.0.2)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.2)
mgcv 1.8-36 2021-06-01 [1] CRAN (R 4.0.2)
mime 0.10 2021-02-13 [1] CRAN (R 4.0.2)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2)
minqa 1.2.4 2014-10-09 [1] CRAN (R 4.0.2)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2)
multcomp 1.4-17 2021-04-29 [1] CRAN (R 4.0.5)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
mvtnorm 1.1-2 2021-06-07 [1] CRAN (R 4.0.2)
nlme 3.1-152 2021-02-04 [1] CRAN (R 4.0.5)
nloptr 1.2.2.2 2020-07-02 [1] CRAN (R 4.0.2)
parameters 0.14.0 2021-05-29 [1] CRAN (R 4.0.2)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.2)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.2)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.5)
projpred 2.0.2 2020-10-28 [1] CRAN (R 4.0.2)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.2)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.2)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
Rcpp * 1.0.6 2021-01-15 [1] CRAN (R 4.0.2)
RcppParallel 5.1.4 2021-05-04 [1] CRAN (R 4.0.2)
readr * 1.4.0 2020-10-05 [1] CRAN (R 4.0.2)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.0.2)
reprex 2.0.0 2021-04-02 [1] CRAN (R 4.0.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2)
rlang 0.4.11.9000 2021-06-12 [1] Github (r-lib/rlang@b501cf7)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
rsconnect 0.8.18 2021-05-24 [1] CRAN (R 4.0.5)
rstan 2.21.3 2021-06-12 [1] Github (stan-dev/rstan@da2fc9c)
rstantools 2.1.1 2020-07-06 [1] CRAN (R 4.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
rvest 1.0.0 2021-03-09 [1] CRAN (R 4.0.2)
sandwich 3.0-1 2021-05-18 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
shiny 1.6.0 2021-01-25 [1] CRAN (R 4.0.2)
shinyjs 2.0.0 2020-09-09 [1] CRAN (R 4.0.2)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 4.0.2)
shinythemes 1.2.0 2021-01-25 [1] CRAN (R 4.0.2)
StanHeaders 2.26.1 2021-04-17 [1] local
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.0.2)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
survival 3.2-11 2021-04-26 [1] CRAN (R 4.0.2)
svUnit 1.0.6 2021-04-19 [1] CRAN (R 4.0.2)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.2)
TH.data 1.0-10 2019-01-21 [1] CRAN (R 4.0.2)
threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.2)
tibble * 3.1.2 2021-05-16 [1] CRAN (R 4.0.2)
tidybayes * 2.3.1 2020-11-02 [1] CRAN (R 4.0.2)
tidyr * 1.1.3 2021-03-03 [1] CRAN (R 4.0.2)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.0.5)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.0.2)
usethis * 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.2)
V8 3.4.2 2021-05-01 [1] CRAN (R 4.0.2)
vctrs 0.3.8.9000 2021-06-12 [1] Github (r-lib/vctrs@faccc3a)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.2)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
xts 0.12.1 2020-09-09 [1] CRAN (R 4.0.2)
zoo 1.8-9 2021-03-09 [1] CRAN (R 4.0.2)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
Reproducible example:
set.seed(123)
y <- rbinom(30, size = 1, prob = 0.2016)
# Fitting a simple binomial model using Stan
library(rstan)
model_string <- "
data {
int n;
int y[n];
}
parameters {
real<lower=0, upper=1> theta;
}
model {
y ~ bernoulli(theta);
}"
stan_samples <- stan(model_code = model_string, data = list(y = y, n = length(y)) )
If just run with one chain, this crashes in RStudio. In R, a prompt appears "selection:" and R crashes regardless of the choice (it's unclear what the choices are so I tried "1" and "2"; not entering anything repeats the prompt).
Can confirm updating to R 4.1 from R 4.0.x and reinstalling RStan on MacOS Big Sur has fixed this problem for me.
If install from CRAN, I don't get this problem. If I clone the latest develop from git and install from the local directory, I get warning and error
> 'config' variable 'CPP' is defunct
Warning message:
In system(paste(CPP, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
error in running command
RStan in CRAN says Published: 2021-12-19, but NEWS tells the latest change is Fri July 24 2020. git repo has develop as the default branch, but there is no tag indicating which version is 2.21.3. I'm confused!
> sessionInfo()
R version 4.1.2 (2021-11-01)
...
other attached packages:
[1] rstan_2.21.3 posterior_1.2.0 bayesplot_1.8.1
[4] ggplot2_3.3.5 StanHeaders_2.21.0-7 dplyr_1.0.8
[7] tidyr_1.2.0
EDIT: added relevant sessionInfo
