jburos
commented
3 years ago Here is the output of running check on this branch: Status: 2 ERRORs, 2 WARNINGs, 4 NOTEs
==> roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
ℹ Loading rstanarm
Warning: [/Users/jburos/projects/rstanarm/R/posterior_survfit.R:299] @examples mismatched braces or quotes
Warning: [/Users/jburos/projects/rstanarm/R/posterior_survfit.R:1131] @examples mismatched braces or quotes
Warning: [/Users/jburos/projects/rstanarm/R/posterior_traj.R:183] @examples mismatched braces or quotes
Warning: [/Users/jburos/projects/rstanarm/R/posterior_traj.R:545] @examples mismatched braces or quotes
Warning: [/Users/jburos/projects/rstanarm/R/ps_check.R:71] @examples mismatched braces or quotes
Writing NAMESPACE
Writing NAMESPACE
Documentation completed
==> R CMD build rstanarm
* checking for file ‘rstanarm/DESCRIPTION’ ... OK
* preparing ‘rstanarm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘rstanarm_2.21.2.tar.gz’
==> R CMD check --run-dontrun --run-donttest rstanarm_2.21.2.tar.gz
* using log directory ‘/Users/jburos/projects/rstanarm.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest’
* checking for file ‘rstanarm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rstanarm’ version ‘2.21.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rstanarm’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 28.7Mb
sub-directories of 1Mb or more:
R 2.0Mb
doc 7.8Mb
libs 18.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RcppParallel’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pp_data_surv: no visible binding for global variable ‘xlevs’
stan_surv: no visible binding for global variable ‘xlevs’
Undefined global functions or variables:
xlevs
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Package unavailable to check Rd xrefs: ‘biglm’
Missing link or links in documentation object 'tve.Rd':
‘stanreg’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'stan_surv'
‘prior_covariance’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rstanarm-Ex.R’ failed
sh: line 1: 67023 Segmentation fault: 11 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --encoding=UTF-8 > 'rstanarm-Ex.Rout' 2>&1 < 'rstanarm-Ex.R'
The error most likely occurred in:
> ### Name: pp_validate
> ### Title: Model validation via simulation
> ### Aliases: pp_validate
>
> ### ** Examples
>
> if (.Platform$OS.type != "windows" || .Platform$r_arch != "i386") {
+
+ if (!exists("example_model")) example(example_model)
+ try(pp_validate(example_model)) # fails with default seed / priors
+
+ }
exmpl_> if (.Platform$OS.type != "windows" || .Platform$r_arch != "i386") {
exmpl_+ example_model <-
exmpl_+ stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
exmpl_+ data = lme4::cbpp, family = binomial, QR = TRUE,
exmpl_+ # this next line is only to keep the example small in size!
exmpl_+ chains = 2, cores = 1, seed = 12345, iter = 1000, refresh = 0)
exmpl_+ example_model
exmpl_+ }
stan_glmer
family: binomial [logit]
formula: cbind(incidence, size - incidence) ~ size + period + (1 | herd)
observations: 56
------
Median MAD_SD
(Intercept) -1.5 0.6
size 0.0 0.0
period2 -1.0 0.3
period3 -1.1 0.4
period4 -1.6 0.5
Error terms:
Groups Name Std.Dev.
herd (Intercept) 0.79
Num. levels: herd 15
------
* For help interpreting the printed output see ?print.stanreg
* For info on the priors used see ?prior_summary.stanreg
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: new_CppObject_xp(fields$.module, fields$.pointer, ...)
2: Rcpp::cpp_object_initializer(.self, .refClassDef, ...)
3: .Object$initialize(...)
4: initialize(value, ...)
5: initialize(value, ...)
6: new(stan_fit_cpp_module, data, as.integer(seed), cxxfun)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
11: try(new(stan_fit_cpp_module, data, as.integer(seed), cxxfun))
12: .local(object, ...)
13: (new("nonstandardGenericFunction",
[...] # truncated
27: as.matrix(do.call("update", update_args))
28: pp_validate(example_model)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
33: try(pp_validate(example_model))
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 67334 Segmentation fault: 11 ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
45: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
46: test_code(NULL, exprs, env)
47: source_file(path, child_env(env), wrap = wrap)
48: FUN(X[[i]], ...)
49: lapply(test_paths, test_one_file, env = env, wrap = wrap)
50: force(code)
51: doWithOneRestart(return(expr), restart)
52: withOneRestart(expr, restarts[[1L]])
53: withRestarts(testthat_abort_reporter = function() NULL, force(code))
54: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
55: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
56: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
57: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
58: test_check("rstanarm", invert = FALSE, filter = if (Sys.getenv("NOT_CRAN") != "true") "stan_functions")
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘aov.Rmd’ using ‘UTF-8’... OK
‘betareg.Rmd’ using ‘UTF-8’... OK
‘binomial.Rmd’ using ‘UTF-8’... OK
‘continuous.Rmd’ using ‘UTF-8’... OK
‘count.Rmd’ using ‘UTF-8’... OK
‘glmer.Rmd’ using ‘UTF-8’... OK
‘jm.Rmd’ using ‘UTF-8’... OK
‘lm.Rmd’ using ‘UTF-8’... OK
‘mrp.Rmd’ using ‘UTF-8’... OK
‘polr.Rmd’ using ‘UTF-8’... OK
‘pooling.Rmd’ using ‘UTF-8’... OK
‘priors.Rmd’ using ‘UTF-8’... OK
‘rstanarm.Rmd’ using ‘UTF-8’... OK
‘surv.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 4 NOTEs
See
‘/Users/jburos/projects/rstanarm.Rcheck/00check.log’
for details.
sambrilleman
Address #535 by reversing the order of checks for type in both
model.frame.stanregandformula.stanreg.Note: this breaks behavior of
ranef(), when applied to a stan_surv model with frailty.