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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.
Activity
andrjohns commentedon Feb 24, 2025
What output do you get if you use the standard
install.packages("rstanarm")?lorenzoFabbri commentedon Feb 24, 2025
I obtain the same error message:
andrjohns commentedon Feb 24, 2025
Can you try the installation outside of an active
renvsession? It's still delegating torenv::install()lorenzoFabbri commentedon Feb 24, 2025
For that I need more time because apparently it's having issues installing some packages:
RcppEigenis installed corrently in the R environment. I'll try again.schuettl commentedon Apr 10, 2025
I ran into the same issue on a Ubuntu 20 VM. I can install the package outside my renv environment. But it gives the same error when installing via renv.
andrjohns commentedon Apr 10, 2025
If it can be installed normally but fails to install under
renv, then there's likely somerenv-specific configuration or issue. I think your best would be to open an issue in therenvgithub: https://github.com/rstudio/renv/issues