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{renv} 0.17.0 cannot find rmarkdown on hydrate with bare project on CI #1161

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zkamvar opened this issue Mar 8, 2023 · 11 comments
Closed

{renv} 0.17.0 cannot find rmarkdown on hydrate with bare project on CI #1161

zkamvar opened this issue Mar 8, 2023 · 11 comments

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@zkamvar
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zkamvar commented Mar 8, 2023

I'm having a problem with {sandpaper}, which uses {renv} to provision a non-invasive dependencies for lessons.

I'm finding an odd situation: on Continuous integration, and ONLY on R > 4.2 and < 4.0, {renv} can not detect {rmarkdown} during bootstrap.

During bootstrap, I do the following steps:

  1. initialise the project containing R Markdown files with a bare renv with a named profile
  2. run hydrate to capture all packages in the project
  3. snapshot

However, with the latest version of {renv}, I've noticed problems with the bootstrap hydration phase:

  * Discovering package dependencies ... Done!
  The following packages are used in this project, but not available locally:
  
  	rmarkdown
  
  renv will attempt to download and install these packages.
  
  * Hydrated 0 packages in 0.005 milliseconds.

But when I run renv::diagnostics(), {rmarkdown} is available locally:

diagnostics report 
Diagnostics Report [renv 0.17.0-27]
  ===================================
  
  # Session Info =======================
  R version 4.2.2 (2022-10-31)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Ubuntu 22.04.2 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=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
   [4] LC_COLLATE=C           LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
   [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
  [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
  [1] compiler_4.2.2 cli_3.6.0      tools_4.2.2    yaml_2.3.7     renv_0.17.0-27
  
  # Project ============================
  Project path: "/tmp/RtmpzoFKmi/working_dir/RtmpaXzVNh/file33036bcd010a/lesson-example"
  
  # Status =============================
  * This project has not yet been snapshotted -- 'renv.lock' does not exist.
  The following package(s) are installed, but not recorded in the lockfile:
              _
    knitr       [1.42]
    magrittr    [2.0.3]
    rappdirs    [0.3.3]
    R6          [2.5.1]
    rlang       [1.0.6]
    fastmap     [1.1.1]
    stringr     [1.5.0]
    highr       [0.10]
    xfun        [0.37]
    tinytex     [0.44]
    cli         [3.6.0]
    jquerylib   [0.1.4]
    htmltools   [0.5.4]
    ellipsis    [0.3.2]
    yaml        [2.3.7]
    digest      [0.6.31]
    lifecycle   [1.0.3]
    sass        [0.4.5]
    base64enc   [0.1-3]
    vctrs       [0.5.2]
    fs          [1.6.1]
    memoise     [2.0.1]
    glue        [1.6.2]
    cachem      [1.0.7]
    evaluate    [0.20]
    mime        [0.12]
    rmarkdown   [2.20]
    stringi     [1.7.12]
    bslib       [0.4.2]
    jsonlite    [1.8.4]
    renv        [rstudio/renv@HEAD]
  
  Use `renv::snapshot()` to add these packages to the lockfile.
  
  
  # Packages ===========================
  This project has not yet been snapshotted: 'renv.lock' does not exist.
                 Library      Source Lockfile Source Path Dependency
  KernSmooth     2.23-20        CRAN     <NA>   <NA>  [1]       <NA>
  MASS          7.3-58.1        CRAN     <NA>   <NA>  [1]       <NA>
  Matrix           1.5-1        CRAN     <NA>   <NA>  [1]       <NA>
  R6               2.5.1        RSPM     <NA>   <NA>  [1]   indirect
  Rcpp            1.0.10        RSPM     <NA>   <NA>  [1]       <NA>
  askpass            1.1        RSPM     <NA>   <NA>  [1]       <NA>
  assertthat       0.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  base64enc        0.1-3        RSPM     <NA>   <NA>  [1]   indirect
  boot            1.3-28        CRAN     <NA>   <NA>  [1]       <NA>
  brio             1.1.3        RSPM     <NA>   <NA>  [1]       <NA>
  bslib            0.4.2        RSPM     <NA>   <NA>  [1]   indirect
  cachem           1.0.7        RSPM     <NA>   <NA>  [1]   indirect
  callr            3.7.3        RSPM     <NA>   <NA>  [1]       <NA>
  class           7.3-20        CRAN     <NA>   <NA>  [1]       <NA>
  cli              3.6.0        RSPM     <NA>   <NA>  [1]   indirect
  clipr            0.8.0        RSPM     <NA>   <NA>  [1]       <NA>
  cluster          2.1.4        CRAN     <NA>   <NA>  [1]       <NA>
  codetools       0.2-18        CRAN     <NA>   <NA>  [2]       <NA>
  commonmark       1.8.1        RSPM     <NA>   <NA>  [1]       <NA>
  covr             3.6.1        RSPM     <NA>   <NA>  [1]       <NA>
  cpp11            0.4.3        RSPM     <NA>   <NA>  [1]       <NA>
  crayon           1.5.2        RSPM     <NA>   <NA>  [1]       <NA>
  credentials      1.3.2        RSPM     <NA>   <NA>  [1]       <NA>
  curl             5.0.0        RSPM     <NA>   <NA>  [1]       <NA>
  desc             1.4.2        RSPM     <NA>   <NA>  [1]       <NA>
  diffobj          0.3.5        RSPM     <NA>   <NA>  [1]       <NA>
  digest          0.6.31        RSPM     <NA>   <NA>  [1]   indirect
  downlit          0.4.2        RSPM     <NA>   <NA>  [1]       <NA>
  ellipsis         0.3.2        RSPM     <NA>   <NA>  [1]   indirect
  evaluate          0.20        RSPM     <NA>   <NA>  [1]   indirect
  fansi            1.0.4        RSPM     <NA>   <NA>  [1]       <NA>
  fastmap          1.1.1        RSPM     <NA>   <NA>  [1]   indirect
  foreign         0.8-83        CRAN     <NA>   <NA>  [1]       <NA>
  fs               1.6.1        RSPM     <NA>   <NA>  [1]   indirect
  gert             1.9.2        RSPM     <NA>   <NA>  [1]       <NA>
  gh               1.4.0        RSPM     <NA>   <NA>  [1]       <NA>
  gitcreds         0.1.2        RSPM     <NA>   <NA>  [1]       <NA>
  glue             1.6.2        RSPM     <NA>   <NA>  [1]   indirect
  grDevices         <NA>        <NA>     <NA>   <NA>  [2]   indirect
  graphics          <NA>        <NA>     <NA>   <NA>  [2]   indirect
  highr             0.10        RSPM     <NA>   <NA>  [1]   indirect
  htmltools        0.5.4        RSPM     <NA>   <NA>  [1]   indirect
  httpuv           1.6.9        RSPM     <NA>   <NA>  [1]       <NA>
  httr             1.4.5        RSPM     <NA>   <NA>  [1]       <NA>
  httr2            0.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  ini              0.3.1        RSPM     <NA>   <NA>  [1]       <NA>
  jquerylib        0.1.4        RSPM     <NA>   <NA>  [1]   indirect
  jsonlite         1.8.4        RSPM     <NA>   <NA>  [1]   indirect
  knitr             1.42        RSPM     <NA>   <NA>  [1]   indirect
  later            1.3.0        RSPM     <NA>   <NA>  [1]       <NA>
  lattice        0.20-45        CRAN     <NA>   <NA>  [1]       <NA>
  lazyeval         0.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  lifecycle        1.0.3        RSPM     <NA>   <NA>  [1]   indirect
  magrittr         2.0.3        RSPM     <NA>   <NA>  [1]   indirect
  markdown           1.5        RSPM     <NA>   <NA>  [1]       <NA>
  memoise          2.0.1        RSPM     <NA>   <NA>  [1]   indirect
  methods           <NA>        <NA>     <NA>   <NA>  [2]   indirect
  mgcv            1.8-41        CRAN     <NA>   <NA>  [1]       <NA>
  mime              0.12        RSPM     <NA>   <NA>  [1]   indirect
  mockr            0.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  nlme           3.1-160        CRAN     <NA>   <NA>  [1]       <NA>
  nnet            7.3-18        CRAN     <NA>   <NA>  [1]       <NA>
  openssl          2.0.5        RSPM     <NA>   <NA>  [1]       <NA>
  pegboard         0.4.3      GitHub     <NA>   <NA>  [1]       <NA>
  pillar           1.8.1        RSPM     <NA>   <NA>  [1]       <NA>
  pkgconfig        2.0.3        RSPM     <NA>   <NA>  [1]       <NA>
  pkgdown          2.0.7        RSPM     <NA>   <NA>  [1]       <NA>
  pkgload          1.3.2        RSPM     <NA>   <NA>  [1]       <NA>
  praise           1.0.0        RSPM     <NA>   <NA>  [1]       <NA>
  processx         3.8.0        RSPM     <NA>   <NA>  [1]       <NA>
  promises       1.2.0.1        RSPM     <NA>   <NA>  [1]       <NA>
  ps               1.7.2        RSPM     <NA>   <NA>  [1]       <NA>
  purrr            1.0.1        RSPM     <NA>   <NA>  [1]       <NA>
  ragg             1.2.5        RSPM     <NA>   <NA>  [1]       <NA>
  rappdirs         0.3.3        RSPM     <NA>   <NA>  [1]   indirect
  rematch2         2.1.2        RSPM     <NA>   <NA>  [1]       <NA>
  renv         0.17.0-27      GitHub     <NA>   <NA>  [1]       <NA>
  rex              1.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  rlang            1.0.6        RSPM     <NA>   <NA>  [1]   indirect
  rmarkdown         2.20        RSPM     <NA>   <NA>  [1]     direct
  rpart           4.1.19        CRAN     <NA>   <NA>  [1]       <NA>
  rprojroot        2.0.3        RSPM     <NA>   <NA>  [1]       <NA>
  rstudioapi        0.14        RSPM     <NA>   <NA>  [1]       <NA>
  sandpaper       0.11.7 carpentries     <NA>   <NA>  [1]       <NA>
  sass             0.4.5        RSPM     <NA>   <NA>  [1]   indirect
  servr             0.25        RSPM     <NA>   <NA>  [1]       <NA>
  sessioninfo      1.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  spatial         7.3-15        CRAN     <NA>   <NA>  [1]       <NA>
  stats             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  stringi         1.7.12        RSPM     <NA>   <NA>  [1]   indirect
  stringr          1.5.0        RSPM     <NA>   <NA>  [1]   indirect
  survival         3.4-0        CRAN     <NA>   <NA>  [1]       <NA>
  sys              3.4.1        RSPM     <NA>   <NA>  [1]       <NA>
  systemfonts      1.0.4        RSPM     <NA>   <NA>  [1]       <NA>
  testthat         3.1.6        RSPM     <NA>   <NA>  [1]       <NA>
  textshaping      0.3.6        RSPM     <NA>   <NA>  [1]       <NA>
  tibble           3.2.0        CRAN     <NA>   <NA>  [1]       <NA>
  tinkr       0.1.0.9000      GitHub     <NA>   <NA>  [1]       <NA>
  tinytex           0.44        RSPM     <NA>   <NA>  [1]   indirect
  tools             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  usethis          2.1.6        RSPM     <NA>   <NA>  [1]       <NA>
  utf8             1.2.3        RSPM     <NA>   <NA>  [1]       <NA>
  utils             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  varnish         0.2.14      GitHub     <NA>   <NA>  [1]       <NA>
  vctrs            0.5.2        RSPM     <NA>   <NA>  [1]   indirect
  waldo            0.4.0        RSPM     <NA>   <NA>  [1]       <NA>
  whisker          0.4.1        RSPM     <NA>   <NA>  [1]       <NA>
  withr            2.5.0        RSPM     <NA>   <NA>  [1]       <NA>
  xfun              0.37        RSPM     <NA>   <NA>  [1]   indirect
  xml2             1.3.3        RSPM     <NA>   <NA>  [1]       <NA>
  xslt             1.4.4        RSPM     <NA>   <NA>  [1]       <NA>
  yaml             2.3.7        RSPM     <NA>   <NA>  [1]   indirect
  zip              2.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  
  [1]: /tmp/RtmpzoFKmi/RLIBS_1931164ef33f
  [2]: /opt/R/4.2.2/lib/R/library        
  
  # ABI ================================
  * No ABI conflicts were detected in the set of installed packages.
  
  # User Profile =======================
  [1] Source  Package Require Version Dev    
  <0 rows> (or 0-length row.names)
  
  # Settings ===========================
  List of 10
   $ bioconductor.version     : chr(0) 
   $ external.libraries       : chr(0) 
   $ ignored.packages         : chr(0) 
   $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
   $ r.version                : chr(0) 
   $ snapshot.type            : chr "implicit"
   $ use.cache                : logi TRUE
   $ vcs.ignore.cellar        : logi TRUE
   $ vcs.ignore.library       : logi TRUE
   $ vcs.ignore.local         : logi TRUE
  
  # Options ============================
  List of 8
   $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
   $ download.file.method                : NULL
   $ download.file.extra                 : NULL
   $ install.packages.compile.from.source: NULL
   $ pkgType                             : chr "source"
   $ repos                               : Named chr [1:3] "https://carpentries.r-universe.dev/" "https://carpentries.github.io/drat" "https://cran.rstudio.com"
    ..- attr(*, "names")= chr [1:3] "carpentries" "carpentries_archive" "CRAN"
   $ renv.config.user.profile            : logi FALSE
   $ renv.verbose                        : logi TRUE
  
  # Environment Variables ==============
  HOME                       = /home/runner
  LANG                       = C.UTF-8
  MAKE                       = make
  RENV_CONFIG_CACHE_SYMLINKS = FALSE
  RENV_CONFIG_REPOS_OVERRIDE = https://packagemanager.posit.co/cran/__linux__/jammy/latest
  RENV_PATHS_ROOT            = /home/runner/.local/share/renv
  RENV_PATHS_SANDBOX         = /home/runner/work/_temp/sandbox/
  RENV_PROFILE               = lesson-requirements
  R_LIBS                     = /tmp/RtmpzoFKmi/RLIBS_[1931](https://github.com/carpentries/sandpaper/actions/runs/4367134933/jobs/7638060723#step:13:1934)164ef33f
  R_LIBS_SITE                = NULL
  R_LIBS_USER                = NULL
  
  # PATH ===============================
  - /home/runner/work/sandpaper/sandpaper/check/sandpaper.Rcheck/R_check_bin
  - /home/runner/.local/bin
  - /opt/pipx_bin
  - /home/runner/.cargo/bin
  - /home/runner/.config/composer/vendor/bin
  - /usr/local/.ghcup/bin
  - /home/runner/.dotnet/tools
  - /snap/bin
  - /usr/local/sbin
  - /usr/local/bin
  - /usr/sbin
  - /usr/bin
  - /sbin
  - /bin
  - /usr/games
  - /usr/local/games
  - /snap/bin
  
  # Cache ==============================
  There are a total of 114 package(s) installed in the renv cache.
  Cache path: "~/.local/share/renv/cache/v5/R-4.2/x86_64-pc-linux-gnu"
  
  → Recording changes in lockfile
  The following package(s) will be updated in the lockfile:
  
  # GitHub =============================
  - renv   [* -> rstudio/renv@HEAD]
  
  The version of R recorded in the lockfile will be updated:
  - R      [* -> 4.2.2]
  
  * Lockfile written to '/tmp/RtmpzoFKmi/working_dir/RtmpaXzVNh/file33036bcd010a/lesson-example/renv/profiles/lesson-requirements/renv.lock'.
  ℹ Current RENV_PATHS_ROOT /home/runner/.local/share/renv
  ℹ Current renv::paths$root() /home/runner/.local/share/renv
  ℹ ↓ Example lesson in '/tmp/RtmpzoFKmi/working_dir/RtmpaXzVNh/file33036bcd010a/lesson-example'
  ℹ ↑ Local remote in '/tmp/RtmpzoFKmi/working_dir/RtmpaXzVNh/REMOTE-330310e9e5a8'
  i Consent for package cache revoked. Use `use_package_cache()` to undo.
  → Searching for and installing available dependencies
  → Hydrating missing dependencies
  * Discovering package dependencies ... Done!
  The following packages are used in this project, but not available locally:
  
  	rmarkdown
  
  renv will attempt to download and install these packages.
  
  * Hydrated 0 packages in 0.0048 milliseconds.
  $packages
  named list()
  
  $missing
  NULL
  
  Diagnostics Report [renv 0.17.0-27]
  ===================================
  
  # Session Info =======================
  R version 4.2.2 (2022-10-31)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Ubuntu 22.04.2 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=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
   [4] LC_COLLATE=C           LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
   [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
  [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
  [1] compiler_4.2.2 cli_3.6.0      tools_4.2.2    yaml_2.3.7     renv_0.17.0-27
  
  # Project ============================
  Project path: "/tmp/RtmpzoFKmi/working_dir/RtmpaXzVNh/file33031fa1cacd/lesson-init-example"
  
  # Status =============================
  * This project has not yet been snapshotted -- 'renv.lock' does not exist.
  The following package(s) are installed, but not recorded in the lockfile:
              _
    knitr       [1.42]
    magrittr    [2.0.3]
    rappdirs    [0.3.3]
    R6          [2.5.1]
    rlang       [1.0.6]
    fastmap     [1.1.1]
    stringr     [1.5.0]
    highr       [0.10]
    xfun        [0.37]
    tinytex     [0.44]
    cli         [3.6.0]
    jquerylib   [0.1.4]
    htmltools   [0.5.4]
    ellipsis    [0.3.2]
    yaml        [2.3.7]
    digest      [0.6.31]
    lifecycle   [1.0.3]
    sass        [0.4.5]
    base64enc   [0.1-3]
    vctrs       [0.5.2]
    fs          [1.6.1]
    memoise     [2.0.1]
    glue        [1.6.2]
    cachem      [1.0.7]
    evaluate    [0.20]
    mime        [0.12]
    rmarkdown   [2.20]
    stringi     [1.7.12]
    bslib       [0.4.2]
    jsonlite    [1.8.4]
    renv        [rstudio/renv@HEAD]
  
  Use `renv::snapshot()` to add these packages to the lockfile.
  
  
  # Packages ===========================
  This project has not yet been snapshotted: 'renv.lock' does not exist.
                 Library      Source Lockfile Source Path Dependency
  KernSmooth     2.23-20        CRAN     <NA>   <NA>  [1]       <NA>
  MASS          7.3-58.1        CRAN     <NA>   <NA>  [1]       <NA>
  Matrix           1.5-1        CRAN     <NA>   <NA>  [1]       <NA>
  R6               2.5.1        RSPM     <NA>   <NA>  [1]   indirect
  Rcpp            1.0.10        RSPM     <NA>   <NA>  [1]       <NA>
  askpass            1.1        RSPM     <NA>   <NA>  [1]       <NA>
  assertthat       0.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  base64enc        0.1-3        RSPM     <NA>   <NA>  [1]   indirect
  boot            1.3-28        CRAN     <NA>   <NA>  [1]       <NA>
  brio             1.1.3        RSPM     <NA>   <NA>  [1]       <NA>
  bslib            0.4.2        RSPM     <NA>   <NA>  [1]   indirect
  cachem           1.0.7        RSPM     <NA>   <NA>  [1]   indirect
  callr            3.7.3        RSPM     <NA>   <NA>  [1]       <NA>
  class           7.3-20        CRAN     <NA>   <NA>  [1]       <NA>
  cli              3.6.0        RSPM     <NA>   <NA>  [1]   indirect
  clipr            0.8.0        RSPM     <NA>   <NA>  [1]       <NA>
  cluster          2.1.4        CRAN     <NA>   <NA>  [1]       <NA>
  codetools       0.2-18        CRAN     <NA>   <NA>  [2]       <NA>
  commonmark       1.8.1        RSPM     <NA>   <NA>  [1]       <NA>
  covr             3.6.1        RSPM     <NA>   <NA>  [1]       <NA>
  cpp11            0.4.3        RSPM     <NA>   <NA>  [1]       <NA>
  crayon           1.5.2        RSPM     <NA>   <NA>  [1]       <NA>
  credentials      1.3.2        RSPM     <NA>   <NA>  [1]       <NA>
  curl             5.0.0        RSPM     <NA>   <NA>  [1]       <NA>
  desc             1.4.2        RSPM     <NA>   <NA>  [1]       <NA>
  diffobj          0.3.5        RSPM     <NA>   <NA>  [1]       <NA>
  digest          0.6.31        RSPM     <NA>   <NA>  [1]   indirect
  downlit          0.4.2        RSPM     <NA>   <NA>  [1]       <NA>
  ellipsis         0.3.2        RSPM     <NA>   <NA>  [1]   indirect
  evaluate          0.20        RSPM     <NA>   <NA>  [1]   indirect
  fansi            1.0.4        RSPM     <NA>   <NA>  [1]       <NA>
  fastmap          1.1.1        RSPM     <NA>   <NA>  [1]   indirect
  foreign         0.8-83        CRAN     <NA>   <NA>  [1]       <NA>
  fs               1.6.1        RSPM     <NA>   <NA>  [1]   indirect
  gert             1.9.2        RSPM     <NA>   <NA>  [1]       <NA>
  gh               1.4.0        RSPM     <NA>   <NA>  [1]       <NA>
  gitcreds         0.1.2        RSPM     <NA>   <NA>  [1]       <NA>
  glue             1.6.2        RSPM     <NA>   <NA>  [1]   indirect
  grDevices         <NA>        <NA>     <NA>   <NA>  [2]   indirect
  graphics          <NA>        <NA>     <NA>   <NA>  [2]   indirect
  highr             0.10        RSPM     <NA>   <NA>  [1]   indirect
  htmltools        0.5.4        RSPM     <NA>   <NA>  [1]   indirect
  httpuv           1.6.9        RSPM     <NA>   <NA>  [1]       <NA>
  httr             1.4.5        RSPM     <NA>   <NA>  [1]       <NA>
  httr2            0.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  ini              0.3.1        RSPM     <NA>   <NA>  [1]       <NA>
  jquerylib        0.1.4        RSPM     <NA>   <NA>  [1]   indirect
  jsonlite         1.8.4        RSPM     <NA>   <NA>  [1]   indirect
  knitr             1.42        RSPM     <NA>   <NA>  [1]   indirect
  later            1.3.0        RSPM     <NA>   <NA>  [1]       <NA>
  lattice        0.20-45        CRAN     <NA>   <NA>  [1]       <NA>
  lazyeval         0.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  lifecycle        1.0.3        RSPM     <NA>   <NA>  [1]   indirect
  magrittr         2.0.3        RSPM     <NA>   <NA>  [1]   indirect
  markdown           1.5        RSPM     <NA>   <NA>  [1]       <NA>
  memoise          2.0.1        RSPM     <NA>   <NA>  [1]   indirect
  methods           <NA>        <NA>     <NA>   <NA>  [2]   indirect
  mgcv            1.8-41        CRAN     <NA>   <NA>  [1]       <NA>
  mime              0.12        RSPM     <NA>   <NA>  [1]   indirect
  mockr            0.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  nlme           3.1-160        CRAN     <NA>   <NA>  [1]       <NA>
  nnet            7.3-18        CRAN     <NA>   <NA>  [1]       <NA>
  openssl          2.0.5        RSPM     <NA>   <NA>  [1]       <NA>
  pegboard         0.4.3      GitHub     <NA>   <NA>  [1]       <NA>
  pillar           1.8.1        RSPM     <NA>   <NA>  [1]       <NA>
  pkgconfig        2.0.3        RSPM     <NA>   <NA>  [1]       <NA>
  pkgdown          2.0.7        RSPM     <NA>   <NA>  [1]       <NA>
  pkgload          1.3.2        RSPM     <NA>   <NA>  [1]       <NA>
  praise           1.0.0        RSPM     <NA>   <NA>  [1]       <NA>
  processx         3.8.0        RSPM     <NA>   <NA>  [1]       <NA>
  promises       1.2.0.1        RSPM     <NA>   <NA>  [1]       <NA>
  ps               1.7.2        RSPM     <NA>   <NA>  [1]       <NA>
  purrr            1.0.1        RSPM     <NA>   <NA>  [1]       <NA>
  ragg             1.2.5        RSPM     <NA>   <NA>  [1]       <NA>
  rappdirs         0.3.3        RSPM     <NA>   <NA>  [1]   indirect
  rematch2         2.1.2        RSPM     <NA>   <NA>  [1]       <NA>
  renv         0.17.0-27      GitHub     <NA>   <NA>  [1]       <NA>
  rex              1.2.1        RSPM     <NA>   <NA>  [1]       <NA>
  rlang            1.0.6        RSPM     <NA>   <NA>  [1]   indirect
  rmarkdown         2.20        RSPM     <NA>   <NA>  [1]     direct
  rpart           4.1.19        CRAN     <NA>   <NA>  [1]       <NA>
  rprojroot        2.0.3        RSPM     <NA>   <NA>  [1]       <NA>
  rstudioapi        0.14        RSPM     <NA>   <NA>  [1]       <NA>
  sandpaper       0.11.7 carpentries     <NA>   <NA>  [1]       <NA>
  sass             0.4.5        RSPM     <NA>   <NA>  [1]   indirect
  servr             0.25        RSPM     <NA>   <NA>  [1]       <NA>
  sessioninfo      1.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  spatial         7.3-15        CRAN     <NA>   <NA>  [1]       <NA>
  stats             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  stringi         1.7.12        RSPM     <NA>   <NA>  [1]   indirect
  stringr          1.5.0        RSPM     <NA>   <NA>  [1]   indirect
  survival         3.4-0        CRAN     <NA>   <NA>  [1]       <NA>
  sys              3.4.1        RSPM     <NA>   <NA>  [1]       <NA>
  systemfonts      1.0.4        RSPM     <NA>   <NA>  [1]       <NA>
  testthat         3.1.6        RSPM     <NA>   <NA>  [1]       <NA>
  textshaping      0.3.6        RSPM     <NA>   <NA>  [1]       <NA>
  tibble           3.2.0        CRAN     <NA>   <NA>  [1]       <NA>
  tinkr       0.1.0.9000      GitHub     <NA>   <NA>  [1]       <NA>
  tinytex           0.44        RSPM     <NA>   <NA>  [1]   indirect
  tools             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  usethis          2.1.6        RSPM     <NA>   <NA>  [1]       <NA>
  utf8             1.2.3        RSPM     <NA>   <NA>  [1]       <NA>
  utils             <NA>        <NA>     <NA>   <NA>  [2]   indirect
  varnish         0.2.14      GitHub     <NA>   <NA>  [1]       <NA>
  vctrs            0.5.2        RSPM     <NA>   <NA>  [1]   indirect
  waldo            0.4.0        RSPM     <NA>   <NA>  [1]       <NA>
  whisker          0.4.1        RSPM     <NA>   <NA>  [1]       <NA>
  withr            2.5.0        RSPM     <NA>   <NA>  [1]       <NA>
  xfun              0.37        RSPM     <NA>   <NA>  [1]   indirect
  xml2             1.3.3        RSPM     <NA>   <NA>  [1]       <NA>
  xslt             1.4.4        RSPM     <NA>   <NA>  [1]       <NA>
  yaml             2.3.7        RSPM     <NA>   <NA>  [1]   indirect
  zip              2.2.2        RSPM     <NA>   <NA>  [1]       <NA>
  
  [1]: /tmp/RtmpzoFKmi/RLIBS_1931164ef33f
  [2]: /opt/R/4.2.2/lib/R/library        
  
  # ABI ================================
  * No ABI conflicts were detected in the set of installed packages.
  
  # User Profile =======================
  [1] Source  Package Require Version Dev    
  <0 rows> (or 0-length row.names)
  
  # Settings ===========================
  List of 10
   $ bioconductor.version     : chr(0) 
   $ external.libraries       : chr(0) 
   $ ignored.packages         : chr(0) 
   $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
   $ r.version                : chr(0) 
   $ snapshot.type            : chr "implicit"
   $ use.cache                : logi TRUE
   $ vcs.ignore.cellar        : logi TRUE
   $ vcs.ignore.library       : logi TRUE
   $ vcs.ignore.local         : logi TRUE
  
  # Options ============================
  List of 8
   $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
   $ download.file.method                : NULL
   $ download.file.extra                 : NULL
   $ install.packages.compile.from.source: NULL
   $ pkgType                             : chr "source"
   $ repos                               : Named chr [1:3] "https://carpentries.r-universe.dev/" "https://carpentries.github.io/drat" "https://cran.rstudio.com/"
    ..- attr(*, "names")= chr [1:3] "carpentries" "carpentries_archive" "CRAN"
   $ renv.config.user.profile            : logi FALSE
   $ renv.verbose                        : logi TRUE
  
  # Environment Variables ==============
  HOME                       = /home/runner
  LANG                       = C.UTF-8
  MAKE                       = make
  RENV_CONFIG_CACHE_SYMLINKS = FALSE
  RENV_CONFIG_REPOS_OVERRIDE = https://packagemanager.posit.co/cran/__linux__/jammy/latest
  RENV_PATHS_ROOT            = /home/runner/.local/share/renv
  RENV_PATHS_SANDBOX         = /home/runner/work/_temp/sandbox/
  RENV_PROFILE               = lesson-requirements
  R_LIBS                     = /tmp/RtmpzoFKmi/RLIBS_1931164ef33f
  R_LIBS_SITE                = NULL
  R_LIBS_USER                = NULL
  
  # PATH ===============================
  - /home/runner/work/sandpaper/sandpaper/check/sandpaper.Rcheck/R_check_bin
  - /home/runner/.local/bin
  - /opt/pipx_bin
  - /home/runner/.cargo/bin
  - /home/runner/.config/composer/vendor/bin
  - /usr/local/.ghcup/bin
  - /home/runner/.dotnet/tools
  - /snap/bin
  - /usr/local/sbin
  - /usr/local/bin
  - /usr/sbin
  - /usr/bin
  - /sbin
  - /bin
  - /usr/games
  - /usr/local/games
  - /snap/bin
  
  # Cache ==============================
  There are a total of 114 package(s) installed in the renv cache.
  Cache path: "~/.local/share/renv/cache/v5/R-4.2/x86_64-pc-linux-gnu"

Do you have any advice of where I can look to debug?
@zkamvar zkamvar mentioned this issue Mar 8, 2023
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@kevinushey
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Any chance you can share a reproducible example? The output of the following might also be useful:

find.packages("rmarkdown")
.libPaths()
renv:::renv_libpaths_user()
renv:::renv_libpaths_site()

And perhaps:

renv:::renv_hydrate_dependencies(getwd())
renv:::renv_hydrate_libpaths()

@zkamvar
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zkamvar commented Mar 8, 2023

Any chance you can share a reproducible example?

😅 I can only get it to trigger on R CMD check, so it's one of those awkward situations where I'm trying to pick up a grain of rice with chopsticks attached to baseball bats.

I'll insert those commands and see what output I can get.

zkamvar added a commit to carpentries/sandpaper that referenced this issue Mar 8, 2023
@zkamvar
add diagnostic suggestions from Kevin
29edaa8 
rstudio/renv#1161 (comment)
@zkamvar
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zkamvar commented Mar 9, 2023

That's.... interesting. Here's the output on r-devel:

  The following packages are used in this project, but not available locally:
  
  	rmarkdown
  
  renv will attempt to download and install these packages.
  
  * Hydrated 0 packages in 0.0055 milliseconds.
  
  ── renv diagnostics ────────────────────────────────────────────────────────────
  
  ── find.package ──
  
  [1] "/tmp/RtmpjB6CA6/RLIBS_1d2b6a5e5492/rmarkdown"
  ── libPaths() ──
  [1] "/tmp/RtmpjB6CA6/RLIBS_1d2b6a5e5492" "/opt/R/devel/lib/R/library"        
  
  ── renv_libpaths_user() ──
  [1] "NULL"
  
  ── renv_libpaths_site() ──
  character(0)
  
  ── renv_hydrate_dependencies() ──
  * Discovering package dependencies ... 
  Done!
  list()
  ── renv_hydrate_libpaths() ──
  
  [1] "NULL"                       "/opt/R/devel/lib/R/library"
  → Recording changes in lockfile

for context, this is what I see on [kraftwerk voice] my home computer:

── renv diagnostics ────────────────────────────────────────────────────────────

── find.package ──

[1] "/home/zhian/R/library/rmarkdown"
── libPaths() ──

[1] "/home/zhian/R/library"         "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"       "/usr/lib/R/library"
── renv_libpaths_user() ──

[1] "~/R/library"
── renv_libpaths_site() ──
[1] "/usr/local/lib/R/site-library/" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"

── renv_hydrate_dependencies() ──

* Discovering package dependencies ... Done!
list()
── renv_hydrate_libpaths() ──

[1] "/home/zhian/R/library"         "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"       "/usr/lib/R/library"
[5] "/usr/lib/R/library"

@zkamvar
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zkamvar commented Mar 9, 2023 •
edited
Loading

One more context that succeeds: R 4.0.5:

  ── renv diagnostics ────────────────────────────────────────────────────────────
  
  ── find.package ──
  
  [1] "/tmp/Rtmpz4ewKg/RLIBS_17bb13301fed/rmarkdown"
  ── libPaths() ──
  
  [1] "/tmp/Rtmpz4ewKg/RLIBS_17bb13301fed" "/opt/R/4.0.5/lib/R/library"        
  ── renv_libpaths_user() ──
  [1] "/tmp/Rtmpz4ewKg/RLIBS_17bb13301fed"
  
  ── renv_libpaths_site() ──
  character(0)
  
  ── renv_hydrate_dependencies() ──
  * Discovering package dependencies ... 
  Done!
  list()
  ── renv_hydrate_libpaths() ──
  [1] "/tmp/Rtmpz4ewKg/RLIBS_17bb13301fed" "/opt/R/4.0.5/lib/R/library"

@zkamvar
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zkamvar commented Mar 9, 2023

OH HO HO HO!

I think it comes down to the environment variables. Somehow R_LIBS_SITE and R_LIBS_USER are getting set to "NULL" in R 4.2 and devel, but not in R 4.1 and 4.0:

From the failing run on R 4.2:

  # Environment Variables ==============
  HOME                       = /home/runner
  LANG                       = C.UTF-8
  MAKE                       = make
  RENV_CONFIG_CACHE_SYMLINKS = FALSE
  RENV_CONFIG_REPOS_OVERRIDE = https://packagemanager.posit.co/cran/__linux__/jammy/latest
  RENV_PATHS_ROOT            = /home/runner/.local/share/renv
  RENV_PATHS_SANDBOX         = /home/runner/work/_temp/sandbox/
  RENV_PROFILE               = lesson-requirements
  R_LIBS                     = /tmp/Rtmp7WIf4p/RLIBS_18f86d362a92
  R_LIBS_SITE                = NULL
  R_LIBS_USER                = NULL

And from a successful run on R 4.1

  # Environment Variables ==============
  HOME                       = /home/runner
  LANG                       = C.UTF-8
  MAKE                       = make
  RENV_CONFIG_CACHE_SYMLINKS = FALSE
  RENV_CONFIG_REPOS_OVERRIDE = https://packagemanager.posit.co/cran/__linux__/jammy/latest
  RENV_PATHS_ROOT            = /home/runner/.local/share/renv
  RENV_PATHS_SANDBOX         = /home/runner/work/_temp/sandbox/
  RENV_PROFILE               = lesson-requirements
  R_LIBS                     = /tmp/RtmpSLUECL/RLIBS_198d269846c4
  R_LIBS_SITE                = no_such_dir
  R_LIBS_USER                =

zkamvar added a commit to carpentries/sandpaper that referenced this issue Mar 9, 2023
@zkamvar
attempt to unset envvars
9375cd6 
see rstudio/renv#1161 (comment)
@zkamvar
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zkamvar commented Mar 9, 2023

I think the answer to this problem is to add || value == "NULL" to line 150:

renv/R/libpaths.R

Lines 143 to 156 in 31ae17a

renv_libpaths_user <- function() {
# if renv is active, the user library will be saved
envvars <- c("RENV_DEFAULT_R_LIBS_USER", "R_LIBS_USER")
for (envvar in envvars) {
value <- Sys.getenv(envvar, unset = NA)
if (is.na(value) || value == "<NA>" || !nzchar(value))
next
parts <- strsplit(value, .Platform$path.sep, fixed = TRUE)[[1]]
return(parts)
}

I've tested it on my machine and it has restored my ability to check.

Yes, it's hacky and doesn't really get into the root of the issue, but I honestly have no clue why R CMD check is doing things this way.

zkamvar added a commit to zkamvar/renv that referenced this issue Mar 9, 2023
@zkamvar
prevent "NULL" user libpaths
c11687d 
In R CMD check for R >= 4.2, the environment variable R_LIBS_USER somehow gets set to the character NULL.

This is a bandaid for this. See rstudio#1161 (comment)
@zkamvar zkamvar mentioned this issue Mar 9, 2023
Merged
kevinushey pushed a commit that referenced this issue Mar 9, 2023
@zkamvar
prevent "NULL" user libpaths (#1162)
028ccc5 
In R CMD check for R >= 4.2, the environment variable R_LIBS_USER somehow gets set to the character NULL.

This is a bandaid for this. See #1161 (comment)
@zkamvar
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zkamvar commented Mar 9, 2023 •
edited
Loading

It's successful for R 4.0 and up! 🎉 Thank you for the help!

CI is still failing for R < 4.0... it appears to be setting the user lib to one that doesn't exist on the CI... at least it's different than the successful runs. Do you know why that may be?

── renv diagnostics ────────────────────────────────────────────────────────────

── find.package ──

[1] "/tmp/RtmpQWm9v6/RLIBS_1cf17adf5273/rmarkdown"
── libPaths() ──
[1] "/tmp/RtmpQWm9v6/RLIBS_1cf17adf5273" "/opt/R/3.6.3/lib/R/library"        

── renv_libpaths_user() ──
[1] "~/R/x86_64-pc-linux-gnu-library/3.6"

── renv_libpaths_site() ──
character(0)

── renv_hydrate_dependencies() ──
* Discovering package dependencies ... 
Done!
list()
── renv_hydrate_libpaths() ──

[1] "/home/runner/R/x86_64-pc-linux-gnu-library/3.6"
[2] "/opt/R/3.6.3/lib/R/library"

@kevinushey
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Sorry, I don't know...

As a workaround, you can also try passing a custom sources argument to hydrate(), containing the location where your packages should be found?

@kevinushey
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I could also consider having hydrate() search the library paths as were set before renv were activated.

zkamvar added a commit to carpentries/sandpaper that referenced this issue Mar 9, 2023
@zkamvar
add sources to hydrate
2cf403a 
see: rstudio/renv#1161 (comment)
@zkamvar
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zkamvar commented Mar 9, 2023

Sorry, I don't know...

As a workaround, you can also try passing a custom sources argument to hydrate(), containing the location where your packages should be found?

I am happy to report that this solution did indeed fix the remaining problems! 👯

@kevinushey, I cannot speak for the wider R community, but the time and dedication you put into {renv} has made a whole lot of reproducibility issues a lot easier to tackle. The fact that you were able to point me to the right tools to help debug this issue (despite my best efforts at complicating matters 🙈) shows how well-designed {renv} is as a flexible and sensible method for package management. Thank you so much for everything you do 🙌🏼

I could also consider having hydrate() search the library paths as were set before renv were activated.

I saw that you implemented this in c068880 and I can report that on re-running the job, it now works!

@zkamvar zkamvar closed this as completed Mar 9, 2023
@kevinushey
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Great news :-) Thank you for the kinds words; I'm glad that I'm able to play my part!

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