stan-dev / stan-dev/rstanarm

Failure to install on Ubuntu system

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R
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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.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce renv::install("rstanarm") on Ubuntu 22.04 with R 4.4.2, then inspect doc-rstanarm-package.R at line 107 and the roxygen2/R/namespace.R stack trace. Compare the failing roxygen2 processing with the working rstan and brms installations; done means rstanarm installs successfully without the reported NAMESPACE error.

Written by the indexing model from the issue text.

Assessment

Tech stack
r, ubuntu
Domain
build-system
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
32/100

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