snapshot() fails with error message Error in if (package == "R") return() : missing value where TRUE/FALSE needed

[jrisi256]

Hi,

When I try to run renv::snapshot(), it fails with the following error/warning message:

Error in if (package == "R") return() : 
  missing value where TRUE/FALSE needed
In addition: Warning message:
In parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] :
  subscript out of bounds

The diagnostics are below. If I can provide more information, please let me know! Thanks for making such a great package.

> renv::diagnostics()
Diagnostics Report [renv 1.0.11]
================================

# /etc/lsb-release -----------------------------------------------------------
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.5 LTS"

# /etc/os-release ------------------------------------------------------------
PRETTY_NAME="Ubuntu 22.04.5 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.5 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy


# Session Info ---------------------------------------------------------------
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] renv_1.0.11

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.13-1     rstudioapi_0.17.1 magrittr_2.0.3    usethis_3.1.0    
 [5] devtools_2.4.5    pkgload_1.4.0     xtable_1.8-4      R6_2.5.1         
 [9] rlang_1.1.4       fastmap_1.2.0     urlchecker_1.0.1  tools_4.2.2      
[13] pkgbuild_1.4.5    sessioninfo_1.2.2 miniUI_0.1.1.1    cli_3.6.3        
[17] remotes_2.5.0     htmltools_0.5.8.1 ellipsis_0.3.2    yaml_2.3.10      
[21] digest_0.6.37     lifecycle_1.0.4   brio_1.1.5        shiny_1.10.0     
[25] purrr_1.0.2       later_1.4.1       vctrs_0.6.5       htmlwidgets_1.6.4
[29] profvis_0.4.0     fs_1.6.5          promises_1.3.2    testthat_3.2.2   
[33] glue_1.8.0        memoise_2.0.1     cachem_1.1.0      mime_0.12        
[37] compiler_4.2.2    httpuv_1.6.15    

# Project --------------------------------------------------------------------
Project path: "~/Documents/secret_lives_pa"

# Status ---------------------------------------------------------------------
The following package(s) are in an inconsistent state:

 package  installed recorded used
 ellipsis y         y        n   

The following package(s) are out of sync [lockfile != library]:

# CRAN -----------------------------------------------------------------------
- askpass       [1.2.0 != 1.2.1]
- bit           [4.0.5 != 4.5.0.1]
- bit64         [4.0.5 != 4.5.2]
- bitops        [1.0-7 != 1.0-9]
- bslib         [0.6.1 != 0.8.0]
- cachem        [1.0.8 != 1.1.0]
- caTools       [1.18.2 != 1.18.3]
- cli           [3.6.2 != 3.6.3]
- cpp11         [0.4.7 != 0.5.1]
- crayon        [1.5.2 != 1.5.3]
- curl          [5.2.0 != 6.1.0]
- data.table    [1.15.4 != 1.16.4]
- digest        [0.6.34 != 0.6.37]
- evaluate      [1.0.0 != 1.0.1]
- fastmap       [1.1.1 != 1.2.0]
- fontawesome   [0.5.2 != 0.5.3]
- fs            [1.6.3 != 1.6.5]
- glue          [1.7.0 != 1.8.0]
- gtable        [repo: RSPM != CRAN; ver: 0.3.5 != 0.3.6]
- htmltools     [0.5.7 != 0.5.8.1]
- jsonlite      [1.8.8 != 1.8.9]
- knitr         [repo: RSPM != CRAN; ver: 1.48 != 1.49]
- lattice       [0.20-45 != 0.22-6]
- lubridate     [1.9.3 != 1.9.4]
- mgcv          [1.8-41 != 1.9-1]
- nlme          [3.1-162 != 3.1-166]
- openssl       [2.1.1 != 2.3.0]
- pillar        [1.9.0 != 1.10.1]
- processx      [3.8.3 != 3.8.5]
- ps            [1.7.6 != 1.8.1]
- R.oo          [1.26.0 != 1.27.0]
- Rcpp          [1.0.12 != 1.0.13-1]
- rlang         [1.1.3 != 1.1.4]
- rmarkdown     [2.28 != 2.29]
- rvest         [1.0.3 != 1.0.4]
- sass          [0.4.8 != 0.4.9]
- stringi       [1.8.3 != 1.8.4]
- sys           [3.4.2 != 3.4.3]
- tidyselect    [1.2.0 != 1.2.1]
- tinytex       [0.53 != 0.54]
- withr         [3.0.0 != 3.0.2]
- xfun          [0.47 != 0.50]
- yaml          [2.3.8 != 2.3.10]

See `?renv::status` for advice on resolving these issues.

# Packages -------------------------------------------------------------------
Traceback (most recent calls last):
4: renv::diagnostics()
3: tryCatch(reporter(project), error = renv_error_handler) at diagnostics.R#47
2: tryCatchList(expr, classes, parentenv, handlers)
1: tryCatchOne(expr, names, parentenv, handlers[[1L]])

# ABI ------------------------------------------------------------------------
- No ABI problems were detected in the set of installed packages.

# User Profile ---------------------------------------------------------------
[no user profile detected]

# Settings -------------------------------------------------------------------
List of 13
 $ bioconductor.version     : NULL
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr(0) 
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ ppm.enabled              : NULL
 $ ppm.ignored.urls         : NULL
 $ r.version                : NULL
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.cellar        : logi TRUE
 $ vcs.ignore.library       : logi TRUE
 $ vcs.ignore.local         : logi TRUE
 $ vcs.manage.ignores       : logi TRUE

# Options --------------------------------------------------------------------
List of 9
 $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method                : chr "libcurl"
 $ download.file.extra                 : NULL
 $ install.packages.compile.from.source: NULL
 $ pkgType                             : chr "source"
 $ repos                               : Named chr "https://cloud.r-project.org"
  ..- attr(*, "names")= chr "CRAN"
 $ renv.consent                        : logi TRUE
 $ renv.config.updates.parallel        : logi TRUE
 $ renv.verbose                        : logi TRUE

# Environment Variables ------------------------------------------------------
HOME                        = /home/joe
LANG                        = en_US.UTF-8
MAKE                        = make
R_LIBS                      = <NA>
R_LIBS_SITE                 = /opt/R/4.2.2/lib/R/site-library
R_LIBS_USER                 = /home/joe/Documents/secret_lives_pa/renv/library/R-4.2/x86_64-pc-linux-gnu
RENV_DEFAULT_R_ENVIRON      = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS         = <NA>
RENV_DEFAULT_R_LIBS_SITE    = /opt/R/4.2.2/lib/R/site-library
RENV_DEFAULT_R_LIBS_USER    = /home/joe/R/x86_64-pc-linux-gnu-library/4.2
RENV_DEFAULT_R_PROFILE      = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT                = /home/joe/Documents/secret_lives_pa

# PATH -----------------------------------------------------------------------
- /home/joe/Documents/secret_lives_pa/secret_lives_pa_virtenv/bin
- /home/joe/.local/bin
- /opt/python/3.11.0/bin
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /sbin
- /bin
- /usr/games
- /usr/local/games
- /snap/bin
- /usr/lib/rstudio/resources/app/bin/quarto/bin
- /usr/lib/rstudio/resources/app/bin/postback

# Cache ----------------------------------------------------------------------
There are a total of 599 packages installed in the renv cache.
Cache path: "~/.cache/R/renv/cache/v5/R-4.2/x86_64-pc-linux-gnu"

Warning messages:
1: In parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] :
  subscript out of bounds
2: In parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] :
  subscript out of bounds

[kevinushey]

Thanks for the bug report -- is there any chance you can share a reproducible example, or share the project where you're encountering this issue?

[kevinushey]

It might also help to try running with options(warn = 2) set, so that this warning:

In addition: Warning message:
In parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] :
  subscript out of bounds

could be promoted to an error, and then we'll hopefully get a traceback.

[jrisi256]

1. https://github.com/jrisi256/secret_lives_pa --> The link to the project in question where I am experiencing the problems. It is odd because I am not experiencing this problem on my other projects. I tried downgrading to (many) different versions of renv, but none of the older versions worked either. I wish I knew when this problem first popped up. I am not sure what more of a reproducible example I could produce? I start up RStudio, and then the project loads with the following message: Warning message: In parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] :subscript out of bounds. Then, I try and run renv::snapshot() to save the changes made to my lockfile, and then the above error happens.

2. Other steps I tried to fix the problem --> I have run renv::clean(), renv::rebuild(), renv::refresh(), renv::repair(), renv::update(), renv::upgrade(), and renv::deactivate() (and then subsequently re-activating the project). After running these, the problem still remained.

3. Interestingly, I also cannot run renv::scaffold() or renv::init() (when choosing the 2nd option to discard the lockfile). They both produce the original error message.

4. When I set options(warn = 2) and then run renv::snapshot() this is the following traceback I get:

23.
doWithOneRestart(return(expr), restart)
22.
withOneRestart(expr, restarts[[1L]])
21.
withRestarts({
.Internal(.signalCondition(cond, message, call))
.Internal(.dfltWarn(message, call))
}, muffleWarning = function() NULL)
20.
warning(cnd) at utils.R#589
19.
warnify(status) at dependencies.R#501
18.
signalCondition(warnify(status)) at dependencies.R#501
17.
FUN(X[[i]], ...)
16.
lapply(x, f, ...) at utils-map.R#3
15.
bapply(paths, renv_dependencies_discover_impl) at dependencies.R#476
14.
renv_dependencies_discover(files, progress, errors) at dependencies.R#246
13.
renv_dependencies_impl(path = path, root = project, field = "Package",
errors = config$dependency.errors(), dev = dev) at snapshot.R#1012
12.
withCallingHandlers(renv_dependencies_impl(path = path, root = project,
field = "Package", errors = config$dependency.errors(), dev = dev),
renv.dependencies.problems = function(cnd) {
if (identical(config$dependency.errors(), "ignored")) ... at snapshot.R#1012
11.
renv_snapshot_dependencies_impl(project, type, dev) at snapshot.R#968
10.
the$dynamic_objects[[id]] %||% {
dlog("dynamic", "memoizing dynamic value for '%s'", id)
value
} at dynamic.R#57
9.
dynamic(list(project = project, type = type, dev = dev), renv_snapshot_dependencies_impl(project,
type, dev)) at snapshot.R#968
8.
renv_snapshot_dependencies(project = project, type = type, dev = dev) at lockfile.R#194
7.
packages %||% renv_snapshot_dependencies(project = project, type = type,
dev = dev) at lockfile.R#194
6.
renv_lockfile_create_impl(project, type, libpaths, packages,
exclude, prompt, force, dev = dev) at lockfile.R#180
5.
doWithOneRestart(return(expr), restart)
4.
withOneRestart(expr, restarts[[1L]])
3.
withRestarts(renv_lockfile_create_impl(project, type, libpaths,
packages, exclude, prompt, force, dev = dev), renv_recompute_records = function() {
renv_dynamic_reset()
renv_lockfile_create_impl(project, type, libpaths, packages, ... at lockfile.R#180
2.
renv_lockfile_create(project = project, type = type, libpaths = libpaths,
packages = packages, exclude = exclude, prompt = prompt,
force = force, dev = dev) at snapshot.R#176
1.
renv::snapshot()

[jrisi256]

Well, I figured out the issue.

https://github.com/jrisi256/secret_lives_pa/blob/main/pdf_parsing/src/dockets/test_extraction_code.ipynb

When I remove this file, renv::snapshot() works well. A collaborator must have made this file because I do not recognize it. It seems like an empty .ipynb file? Do you know why this would be causing renv to crash? I will hold off on pushing my changes to the project so you can see the file for yourself.

[kevinushey]

Aha, thanks!

renv also attempts to parse R package dependencies from .ipynb files within a project, but is evidently having trouble with empty / invalid files in this scenario. I'll get this fixed up; I appreciate your taking the time to find the underlying cause!