Failure to install on Ubuntu system #634
Description
> renv::install("rstanarm")
# Downloading packages --------------------------------------
- Downloading rstanarm from CRAN ... OK [file is up to date]
Successfully downloaded 1 package in 0.8 seconds.
The following package(s) will be installed:
- rstanarm [2.32.1]
These packages will be installed into "~/Documents/edu/phd/papers/paper-athlete-neuro/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".
Do you want to proceed? [Y/n]: Y
# Installing packages ---------------------------------------
- Installing rstanarm ... FAILED
Error: Error installing package 'rstanarm':
====================================
* installing *source* package ‘rstanarm’ ...
** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
Setting `RoxygenNote` to "7.3.2"
Writing 'NAMESPACE'
Loading required package: Rcpp
Loading required package: bayesplot
This is bayesplot version 1.11.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
Loading required package: ggplot2
Loading required package: lme4
Loading required package: Matrix
Loading required package: loo
This is loo version 2.8.0
- Online documentation and vignettes at mc-stan.org/loo
- As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
Loading required package: nlme
Attaching package: ‘nlme’
The following object is masked from ‘package:lme4’:
lmList
Loading required package: posterior
This is posterior version 1.6.0
Attaching package: ‘posterior’
The following object is masked from ‘package:bayesplot’:
rhat
The following objects are masked from ‘package:stats’:
mad, sd, var
The following objects are masked from ‘package:base’:
%in%, match
Loading required package: rstan
Loading required package: StanHeaders
rstan version 2.32.6 (Stan version 2.32.2)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
change `threads_per_chain` option:
rstan_options(threads_per_chain = 1)
Attaching package: ‘rstan’
The following objects are masked from ‘package:posterior’:
ess_bulk, ess_tail
Loading required package: rstantools
This is rstantools version 2.4.0
Loading required package: shinystan
Loading required package: shiny
This is shinystan version 2.6.0
Loading required package: survival
Loading required package: RcppParallel
Attaching package: ‘RcppParallel’
The following object is masked from ‘package:Rcpp’:
LdFlags
✖ doc-rstanarm-package.R:107: `@docType "package"` is deprecated.
ℹ Please document "_PACKAGE" instead.
Error in `map2()` at roxygen2/R/namespace.R:405:3:
ℹ In index: 1.
ℹ With name: collapse_within_groups.matrix.
Caused by error in `basename()`:
! a character vector argument expected
Backtrace:
▆
1. ├─roxygen2::roxygenize(load_code = roxygen2::load_source, clean = TRUE)
2. │ └─base::lapply(...) at roxygen2/R/roxygenize.R:79:3
3. │ ├─roxygen2 (local) FUN(X[[i]], ...)
4. │ └─roxygen2:::roclet_process.roclet_namespace(X[[i]], ...) at roxygen2/R/roclet.R:56:3
5. │ └─roxygen2:::warn_missing_s3_exports(blocks, env) at roxygen2/R/namespace.R:35:3
6. │ └─purrr::map2(...) at roxygen2/R/namespace.R:405:3
7. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) at purrr/R/map2.R:34:3
8. │ ├─purrr:::with_indexed_errors(...) at purrr/R/map2.R:78:3
9. │ │ └─base::withCallingHandlers(...) at purrr/R/map.R:201:3
10. │ ├─purrr:::call_with_cleanup(...) at purrr/R/map2.R:78:3
11. │ └─roxygen2 (local) .f(.x[[i]], .y[[i]], ...)
12. │ └─roxygen2:::warn_roxy_function(fun, "S3 method {.arg {name}} needs @export or @exportS3method tag") at roxygen2/R/namespace.R:406:5
13. │ └─roxygen2:::warn_roxy(file, line, message, parent = parent, envir = envir) at roxygen2/R/utils-warn.R:21:3
14. │ ├─cli::style_hyperlink(...) at roxygen2/R/utils-warn.R:25:3
15. │ ├─base::paste0(basename(file), ":", line) at roxygen2/R/utils-warn.R:25:3
16. │ └─base::basename(file) at roxygen2/R/utils-warn.R:25:3
17. └─base::.handleSimpleError(...)
18. └─purrr (local) h(simpleError(msg, call))
19. └─cli::cli_abort(...) at purrr/R/map.R:215:9
20. └─rlang::abort(...) at cli/R/rlang.R:45:3
Execution halted
ERROR: a 'NAMESPACE' file is required
* removing ‘/home/lfabbri/Documents/edu/phd/papers/paper-athlete-neuro/renv/staging/2/rstanarm’
install of package 'rstanarm' failed [error code 1]
Traceback (most recent calls last):
12: renv::install("rstanarm")
11: renv_install_impl(records) at install.R#232
10: if (staged)
renv_install_staged(records)
else
renv_install_default(records) at install.R#276
9: renv_install_default(records) at install.R#296
8: handler(package, renv_install_package(record)) at install.R#399
7: handler(package, renv_install_package(record)) at install.R#399
6: withCallingHandlers(
renv_install_package_impl(record),
error = function(e) writef("FAILED")
) at install.R#432
5: withCallingHandlers(
renv_install_package_impl(record),
error = function(e) writef("FAILED")
) at install.R#432
4: if (copyable)
renv_file_copy(path, installpath, overwrite = TRUE)
else
r_cmd_install(package, path) at install.R#643
3: if (!identical(status, 0L))
r_exec_error(package, output, "install", status) at r.R#234
2: abort(all) at r.R#52
1: stop(fallback) at abort.R#44> Sys.info()
sysname
"Linux"
release
"6.8.0-52-generic"
version
"#53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2"
nodename
"ISG10223L"
machine
"x86_64"> R.Version()
$platform
[1] "x86_64-pc-linux-gnu"
$arch
[1] "x86_64"
$os
[1] "linux-gnu"
$system
[1] "x86_64, linux-gnu"
$status
[1] ""
$major
[1] "4"
$minor
[1] "4.2"
$year
[1] "2024"
$month
[1] "10"
$day
[1] "31"
$`svn rev`
[1] "87279"
$language
[1] "R"
$version.string
[1] "R version 4.4.2 (2024-10-31)"
$nickname
[1] "Pile of Leaves"Both rstan and brms seem to be working fine.