renv::restore() does not restore lockfile package versions

[klmr]

Inside an renv project I installed a new version of a package (and numerous updated dependency versions) via renv::install(the_pkg). Unfortunately this caused some issues, so now I want to revert to a known-good version.

So I ran renv::restore(clean = TRUE). The function runs for a while before finishing without creating any output. Unfortunately apparently nothing was done: renv::status() shows me that the lockfile versions of the packages were not restored (see output below). Running renv::restore() repeatedly (with or without clean = TRUE) and restarting the R session does not change this situation.

Am I misunderstanding how renv::restore() is supposed to behave in this situation?

R console output

``` > renv::restore(clean = TRUE) > renv::status() The following package(s) are in an inconsistent state: package installed recorded used httr y y n The following package(s) are out of sync [lockfile != library]: # RSPM --------------------------------------------------------------------- -- - askpass [repo: CRAN != RSPM; ver: 1.1 != 1.2.0] - brio [repo: CRAN != RSPM; ver: 1.1.3 != 1.1.5] - bslib [repo: CRAN != RSPM; ver: 0.5.1 != 0.7.0] - cachem [repo: CRAN != RSPM; ver: 1.0.8 != 1.1.0] - callr [repo: CRAN != RSPM; ver: 3.7.3 != 3.7.6] - cli [repo: CRAN != RSPM; ver: 3.6.1 != 3.6.3] - cpp11 [repo: CRAN != RSPM; ver: 0.4.6 != 0.4.7] - curl [repo: CRAN != RSPM; ver: 5.0.2 != 5.2.1] - desc [repo: CRAN != RSPM; ver: 1.4.2 != 1.4.3] - digest [repo: CRAN != RSPM; ver: 0.6.33 != 0.6.36] - downlit [repo: CRAN != RSPM; ver: 0.4.3 != 0.4.4] - evaluate [repo: CRAN != RSPM; ver: 0.22 != 0.24.0] - fansi [repo: CRAN != RSPM; ver: 1.0.4 != 1.0.6] - fastmap [repo: CRAN != RSPM; ver: 1.1.1 != 1.2.0] - fs [repo: CRAN != RSPM; ver: 1.6.3 != 1.6.4] - glue [repo: CRAN != RSPM; ver: 1.6.2 != 1.7.0] - highr [repo: CRAN != RSPM; ver: 0.10 != 0.11] - htmltools [repo: CRAN != RSPM; ver: 0.5.6 != 0.5.8.1] - httr2 [repo: CRAN != RSPM; ver: 0.2.3 != 1.0.2] - jsonlite [repo: CRAN != RSPM; ver: 1.8.7 != 1.8.8] - knitr [repo: CRAN != RSPM; ver: 1.44 != 1.48] - lifecycle [repo: CRAN != RSPM; ver: 1.0.3 != 1.0.4] - openssl [repo: CRAN != RSPM; ver: 2.0.6 != 2.2.0] - pkgdown [repo: CRAN != RSPM; ver: 2.0.7 != 2.1.0] - processx [repo: CRAN != RSPM; ver: 3.8.2 != 3.8.4] - ps [repo: CRAN != RSPM; ver: 1.7.5 != 1.7.7] - ragg [repo: CRAN != RSPM; ver: 1.2.5 != 1.3.2] - rmarkdown [repo: CRAN != RSPM; ver: 2.25 != 2.27] - sass [repo: CRAN != RSPM; ver: 0.4.7 != 0.4.9] - systemfonts [repo: CRAN != RSPM; ver: 1.0.5 != 1.1.0] - textshaping [repo: CRAN != RSPM; ver: 0.3.7 != 0.4.0] - tinytex [repo: CRAN != RSPM; ver: 0.47 != 0.52] - utf8 [repo: CRAN != RSPM; ver: 1.2.3 != 1.2.4] - withr [repo: CRAN != RSPM; ver: 2.5.0 != 3.0.0] - xfun [repo: CRAN != RSPM; ver: 0.40 != 0.46] - yaml [repo: CRAN != RSPM; ver: 2.3.7 != 2.3.10] See ?renv::status() for advice on resolving these issues. ```

sessionInfo() output

``` R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_GB.UTF-8/UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 time zone: Europe/Zurich tzcode source: internal attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] compiler_4.3.1 tools_4.3.1 yaml_2.3.10 renv_1.0.7 pak_0.7.2 ```

[kevinushey]

This all seems quite unexpected -- renv::restore() should definitely at least be printing a summary of the changes it wants to make, and give you an opportunity to respond.

If you run with the R profiler enabled, e.g. using:

Rprof("renv.Rprof")
renv::restore(clean = TRUE)
Rprof(NULL)
summaryRprof("renv.Rprof")

does the output give you any hints as to what renv is busy doing? (Alternatively, are you able to debug(renv::restore) and step through to see how far you get before the function exits?)

[klmr]

Hm. I now get some output from renv::restore(clean = TRUE), even though nothing in this repository was changed:

✔ Loading metadata database ... done

ℹ No downloads are needed
✔ 1 pkg:  [2.7s]

However, the behaviour is otherwise the same.

Here’s the Rprof output:

summaryRprof("renv.rprof")

``` $by.self self.time self.pct total.time total.pct "unlink" 0.52 33.33 0.52 33.33 "lazyLoadDBfetch" 0.14 8.97 0.24 15.38 "normalizePath" 0.08 5.13 0.08 5.13 "dir.create" 0.06 3.85 0.06 3.85 "file.exists" 0.06 3.85 0.06 3.85 "see_if" 0.06 3.85 0.06 3.85 "rs_run_with_output" 0.04 2.56 0.24 15.38 "rs__get_result_and_output" 0.04 2.56 0.08 5.13 "base::unique" 0.04 2.56 0.04 2.56 "dynGet" 0.04 2.56 0.04 2.56 "renv_json_read_remap" 0.04 2.56 0.04 2.56 "rs__write_for_sure" 0.04 2.56 0.04 2.56 "system2" 0.04 2.56 0.04 2.56 "tryCatch" 0.02 1.28 1.02 65.38 "" 0.02 1.28 0.72 46.15 "rs_call" 0.02 1.28 0.08 5.13 "find.package" 0.02 1.28 0.06 3.85 "file.info" 0.02 1.28 0.04 2.56 ".POSIXct" 0.02 1.28 0.02 1.28 "any" 0.02 1.28 0.02 1.28 "get_result" 0.02 1.28 0.02 1.28 "make_vanilla_script_expr" 0.02 1.28 0.02 1.28 "mode" 0.02 1.28 0.02 1.28 "processx::poll" 0.02 1.28 0.02 1.28 "read_all" 0.02 1.28 0.02 1.28 "renv_filebacked_get" 0.02 1.28 0.02 1.28 "rs__handle_condition" 0.02 1.28 0.02 1.28 "serialize" 0.02 1.28 0.02 1.28 "socketConnection" 0.02 1.28 0.02 1.28 "strsplit" 0.02 1.28 0.02 1.28 "substring" 0.02 1.28 0.02 1.28 $by.total total.time total.pct self.time "renv::restore" 1.56 100.00 0.00 "renv_pak_restore" 1.48 94.87 0.00 "tryCatch" 1.02 65.38 0.02 "doTryCatch" 1.00 64.10 0.00 "tryCatchList" 1.00 64.10 0.00 "tryCatchOne" 1.00 64.10 0.00 "FUN" 0.96 61.54 0.00 "map_lgl" 0.92 58.97 0.00 "vapply" 0.92 58.97 0.00 "renv_cache_synchronize_impl" 0.86 55.13 0.00 "" 0.72 46.15 0.02 "withCallingHandlers" 0.60 38.46 0.00 "eval" 0.58 37.18 0.00 "pak$pkg_install" 0.56 35.90 0.00 "remote" 0.56 35.90 0.00 "unlink" 0.52 33.33 0.52 "restore" 0.52 33.33 0.00 "suppressWarnings" 0.34 21.79 0.00 "new_remote_session" 0.30 19.23 0.00 "restart_remote_if_needed" 0.30 19.23 0.00 "lazyLoadDBfetch" 0.24 15.38 0.14 "rs_run_with_output" 0.24 15.38 0.04 "load_private_package" 0.24 15.38 0.00 "load_private_packages" 0.24 15.38 0.00 "set_function_envs" 0.24 15.38 0.00 "rs$run_with_output" 0.16 10.26 0.00 "load_private_cli" 0.12 7.69 0.00 "..getNamespace" 0.10 6.41 0.00 "force" 0.10 6.41 0.00 "loadNamespace" 0.10 6.41 0.00 "renv_cache_copy" 0.10 6.41 0.00 "renv_file_same" 0.10 6.41 0.00 "normalizePath" 0.08 5.13 0.08 "rs__get_result_and_output" 0.08 5.13 0.04 "rs_call" 0.08 5.13 0.02 "%||%" 0.08 5.13 0.00 "catchall" 0.08 5.13 0.00 "private$get_result_and_output" 0.08 5.13 0.00 "private$parse_msg" 0.08 5.13 0.00 "renv_file_copy_dir" 0.08 5.13 0.00 "renv_file_copy" 0.08 5.13 0.00 "renv_file_move" 0.08 5.13 0.00 "renv_lock_acquire" 0.08 5.13 0.00 "renv_scope_lock" 0.08 5.13 0.00 "rs__parse_msg_funcs[[code]]" 0.08 5.13 0.00 "rs__parse_msg" 0.08 5.13 0.00 "rs_read" 0.08 5.13 0.00 "rs_run" 0.08 5.13 0.00 "rs$run" 0.08 5.13 0.00 "self$call" 0.08 5.13 0.00 "self$read" 0.08 5.13 0.00 "structure" 0.08 5.13 0.00 "dir.create" 0.06 3.85 0.06 "file.exists" 0.06 3.85 0.06 "see_if" 0.06 3.85 0.06 "find.package" 0.06 3.85 0.02 "assert_that" 0.06 3.85 0.00 "catch" 0.06 3.85 0.00 "conn_create_pipepair" 0.06 3.85 0.00 "do.call" 0.06 3.85 0.00 "initialize" 0.06 3.85 0.00 "lapply" 0.06 3.85 0.00 "method" 0.06 3.85 0.00 "process_initialize" 0.06 3.85 0.00 "renv_lock_acquire_impl" 0.06 3.85 0.00 "renv_path_normalize" 0.06 3.85 0.00 "rs_init" 0.06 3.85 0.00 "with_envvar" 0.06 3.85 0.00 "base::unique" 0.04 2.56 0.04 "dynGet" 0.04 2.56 0.04 "renv_json_read_remap" 0.04 2.56 0.04 "rs__write_for_sure" 0.04 2.56 0.04 "system2" 0.04 2.56 0.04 "file.info" 0.04 2.56 0.02 "available_packages" 0.04 2.56 0.00 "dynamic" 0.04 2.56 0.00 "index" 0.04 2.56 0.00 "map" 0.04 2.56 0.00 "paste" 0.04 2.56 0.00 "private$write_for_sure" 0.04 2.56 0.00 "renv_available_packages_impl" 0.04 2.56 0.00 "renv_available_packages_latest_repos_impl" 0.04 2.56 0.00 "renv_available_packages_latest" 0.04 2.56 0.00 "renv_available_packages_query" 0.04 2.56 0.00 "renv_bootstrap_platform_prefix" 0.04 2.56 0.00 "renv_cache_find" 0.04 2.56 0.00 "renv_file_backup" 0.04 2.56 0.00 "renv_file_copy_dir_cp" 0.04 2.56 0.00 "renv_file_copy_dir_impl" 0.04 2.56 0.00 "renv_file_info" 0.04 2.56 0.00 "renv_index_set" 0.04 2.56 0.00 "renv_json_read_default" 0.04 2.56 0.00 "renv_json_read" 0.04 2.56 0.00 "renv_lockfile_read" 0.04 2.56 0.00 "renv_pak_init" 0.04 2.56 0.00 "renv_pak_stream" 0.04 2.56 0.00 "renv_paths_cache" 0.04 2.56 0.00 "renv_platform_prefix" 0.04 2.56 0.00 "renv_system_exec" 0.04 2.56 0.00 "renv_watchdog_notify_impl" 0.04 2.56 0.00 "renv_watchdog_notify" 0.04 2.56 0.00 "unique" 0.04 2.56 0.00 "with.default" 0.04 2.56 0.00 "with" 0.04 2.56 0.00 ".POSIXct" 0.02 1.28 0.02 "any" 0.02 1.28 0.02 "get_result" 0.02 1.28 0.02 "make_vanilla_script_expr" 0.02 1.28 0.02 "mode" 0.02 1.28 0.02 "processx::poll" 0.02 1.28 0.02 "read_all" 0.02 1.28 0.02 "renv_filebacked_get" 0.02 1.28 0.02 "rs__handle_condition" 0.02 1.28 0.02 "serialize" 0.02 1.28 0.02 "socketConnection" 0.02 1.28 0.02 "strsplit" 0.02 1.28 0.02 "substring" 0.02 1.28 0.02 ".make_numeric_version" 0.02 1.28 0.00 "[.numeric_version" 0.02 1.28 0.00 "[" 0.02 1.28 0.00 "base::numeric_version" 0.02 1.28 0.00 "download" 0.02 1.28 0.00 "downloader" 0.02 1.28 0.00 "empty" 0.02 1.28 0.00 "ensure_directory" 0.02 1.28 0.00 "ensure_parent_directory" 0.02 1.28 0.00 "filebacked" 0.02 1.28 0.00 "format.default" 0.02 1.28 0.00 "numeric_version" 0.02 1.28 0.00 "renv_activate_version" 0.02 1.28 0.00 "renv_available_packages_filter_version" 0.02 1.28 0.00 "renv_available_packages_filter" 0.02 1.28 0.00 "renv_available_packages_success" 0.02 1.28 0.00 "renv_defer_get" 0.02 1.28 0.00 "renv_defer_id" 0.02 1.28 0.00 "renv_description_read" 0.02 1.28 0.00 "renv_download_auth_type" 0.02 1.28 0.00 "renv_download_auth" 0.02 1.28 0.00 "renv_download_impl" 0.02 1.28 0.00 "renv_infrastructure_write_activate" 0.02 1.28 0.00 "renv_lock_release_impl" 0.02 1.28 0.00 "renv_lock_release" 0.02 1.28 0.00 "renv_lockfile_load" 0.02 1.28 0.00 "renv_restore_successful" 0.02 1.28 0.00 "renv_scope_tempfile" 0.02 1.28 0.00 "renv_socket_connect" 0.02 1.28 0.00 "startswith" 0.02 1.28 0.00 "tolower" 0.02 1.28 0.00 self.pct "renv::restore" 0.00 "renv_pak_restore" 0.00 "tryCatch" 1.28 "doTryCatch" 0.00 "tryCatchList" 0.00 "tryCatchOne" 0.00 "FUN" 0.00 "map_lgl" 0.00 "vapply" 0.00 "renv_cache_synchronize_impl" 0.00 "" 1.28 "withCallingHandlers" 0.00 "eval" 0.00 "pak$pkg_install" 0.00 "remote" 0.00 "unlink" 33.33 "restore" 0.00 "suppressWarnings" 0.00 "new_remote_session" 0.00 "restart_remote_if_needed" 0.00 "lazyLoadDBfetch" 8.97 "rs_run_with_output" 2.56 "load_private_package" 0.00 "load_private_packages" 0.00 "set_function_envs" 0.00 "rs$run_with_output" 0.00 "load_private_cli" 0.00 "..getNamespace" 0.00 "force" 0.00 "loadNamespace" 0.00 "renv_cache_copy" 0.00 "renv_file_same" 0.00 "normalizePath" 5.13 "rs__get_result_and_output" 2.56 "rs_call" 1.28 "%||%" 0.00 "catchall" 0.00 "private$get_result_and_output" 0.00 "private$parse_msg" 0.00 "renv_file_copy_dir" 0.00 "renv_file_copy" 0.00 "renv_file_move" 0.00 "renv_lock_acquire" 0.00 "renv_scope_lock" 0.00 "rs__parse_msg_funcs[[code]]" 0.00 "rs__parse_msg" 0.00 "rs_read" 0.00 "rs_run" 0.00 "rs$run" 0.00 "self$call" 0.00 "self$read" 0.00 "structure" 0.00 "dir.create" 3.85 "file.exists" 3.85 "see_if" 3.85 "find.package" 1.28 "assert_that" 0.00 "catch" 0.00 "conn_create_pipepair" 0.00 "do.call" 0.00 "initialize" 0.00 "lapply" 0.00 "method" 0.00 "process_initialize" 0.00 "renv_lock_acquire_impl" 0.00 "renv_path_normalize" 0.00 "rs_init" 0.00 "with_envvar" 0.00 "base::unique" 2.56 "dynGet" 2.56 "renv_json_read_remap" 2.56 "rs__write_for_sure" 2.56 "system2" 2.56 "file.info" 1.28 "available_packages" 0.00 "dynamic" 0.00 "index" 0.00 "map" 0.00 "paste" 0.00 "private$write_for_sure" 0.00 "renv_available_packages_impl" 0.00 "renv_available_packages_latest_repos_impl" 0.00 "renv_available_packages_latest" 0.00 "renv_available_packages_query" 0.00 "renv_bootstrap_platform_prefix" 0.00 "renv_cache_find" 0.00 "renv_file_backup" 0.00 "renv_file_copy_dir_cp" 0.00 "renv_file_copy_dir_impl" 0.00 "renv_file_info" 0.00 "renv_index_set" 0.00 "renv_json_read_default" 0.00 "renv_json_read" 0.00 "renv_lockfile_read" 0.00 "renv_pak_init" 0.00 "renv_pak_stream" 0.00 "renv_paths_cache" 0.00 "renv_platform_prefix" 0.00 "renv_system_exec" 0.00 "renv_watchdog_notify_impl" 0.00 "renv_watchdog_notify" 0.00 "unique" 0.00 "with.default" 0.00 "with" 0.00 ".POSIXct" 1.28 "any" 1.28 "get_result" 1.28 "make_vanilla_script_expr" 1.28 "mode" 1.28 "processx::poll" 1.28 "read_all" 1.28 "renv_filebacked_get" 1.28 "rs__handle_condition" 1.28 "serialize" 1.28 "socketConnection" 1.28 "strsplit" 1.28 "substring" 1.28 ".make_numeric_version" 0.00 "[.numeric_version" 0.00 "[" 0.00 "base::numeric_version" 0.00 "download" 0.00 "downloader" 0.00 "empty" 0.00 "ensure_directory" 0.00 "ensure_parent_directory" 0.00 "filebacked" 0.00 "format.default" 0.00 "numeric_version" 0.00 "renv_activate_version" 0.00 "renv_available_packages_filter_version" 0.00 "renv_available_packages_filter" 0.00 "renv_available_packages_success" 0.00 "renv_defer_get" 0.00 "renv_defer_id" 0.00 "renv_description_read" 0.00 "renv_download_auth_type" 0.00 "renv_download_auth" 0.00 "renv_download_impl" 0.00 "renv_infrastructure_write_activate" 0.00 "renv_lock_release_impl" 0.00 "renv_lock_release" 0.00 "renv_lockfile_load" 0.00 "renv_restore_successful" 0.00 "renv_scope_tempfile" 0.00 "renv_socket_connect" 0.00 "startswith" 0.00 "tolower" 0.00 $sample.interval [1] 0.02 $sampling.time [1] 1.56 ```

[kevinushey]

Based on that output, I suspect the issue here lies with how pak is being invoked by renv... do you have better luck with options(renv.config.pak.enabled = FALSE)?

It's also possible this is the same as https://github.com/rstudio/renv/blob/main/NEWS.md?plain=1#L47-L49 -- if that's the case, then this is a bug with how renv is invoking pak, and should be resolved in the development version of renv.

[klmr]

Okay, disabling ‘pak’ did change the behaviour, it asks to restore a bunch of packages, and does so after prompting. However, afterwards the library is still not synchronised, as shown by renv::status():

``` > renv::restore(clean = TRUE) The following package(s) will be updated: # CRAN ----------------------------------------------------------------------- - askpass [repo: RSPM -> CRAN; ver: 1.2.0 -> 1.1] - brio [repo: RSPM -> CRAN; ver: 1.1.5 -> 1.1.3] - bslib [repo: RSPM -> CRAN; ver: 0.7.0 -> 0.5.1] - cachem [repo: RSPM -> CRAN; ver: 1.1.0 -> 1.0.8] - callr [repo: RSPM -> CRAN; ver: 3.7.6 -> 3.7.3] - cli [repo: RSPM -> CRAN; ver: 3.6.3 -> 3.6.1] - cpp11 [repo: RSPM -> CRAN; ver: 0.4.7 -> 0.4.6] - curl [repo: RSPM -> CRAN; ver: 5.2.1 -> 5.0.2] - desc [repo: RSPM -> CRAN; ver: 1.4.3 -> 1.4.2] - digest [repo: RSPM -> CRAN; ver: 0.6.36 -> 0.6.33] - downlit [repo: RSPM -> CRAN; ver: 0.4.4 -> 0.4.3] - evaluate [repo: RSPM -> CRAN; ver: 0.24.0 -> 0.22] - fansi [repo: RSPM -> CRAN; ver: 1.0.6 -> 1.0.4] - fastmap [repo: RSPM -> CRAN; ver: 1.2.0 -> 1.1.1] - fs [repo: RSPM -> CRAN; ver: 1.6.4 -> 1.6.3] - glue [repo: RSPM -> CRAN; ver: 1.7.0 -> 1.6.2] - highr [repo: RSPM -> CRAN; ver: 0.11 -> 0.10] - htmltools [repo: RSPM -> CRAN; ver: 0.5.8.1 -> 0.5.6] - httr2 [repo: RSPM -> CRAN; ver: 1.0.2 -> 0.2.3] - jsonlite [repo: RSPM -> CRAN; ver: 1.8.8 -> 1.8.7] - knitr [repo: RSPM -> CRAN; ver: 1.48 -> 1.44] - lifecycle [repo: RSPM -> CRAN; ver: 1.0.4 -> 1.0.3] - openssl [repo: RSPM -> CRAN; ver: 2.2.0 -> 2.0.6] - pak [0.7.2 -> *] - pkgdown [repo: RSPM -> CRAN; ver: 2.1.0 -> 2.0.7] - processx [repo: RSPM -> CRAN; ver: 3.8.4 -> 3.8.2] - ps [repo: RSPM -> CRAN; ver: 1.7.7 -> 1.7.5] - ragg [repo: RSPM -> CRAN; ver: 1.3.2 -> 1.2.5] - rmarkdown [repo: RSPM -> CRAN; ver: 2.27 -> 2.25] - sass [repo: RSPM -> CRAN; ver: 0.4.9 -> 0.4.7] - systemfonts [repo: RSPM -> CRAN; ver: 1.1.0 -> 1.0.5] - textshaping [repo: RSPM -> CRAN; ver: 0.4.0 -> 0.3.7] - tinytex [repo: RSPM -> CRAN; ver: 0.52 -> 0.47] - utf8 [repo: RSPM -> CRAN; ver: 1.2.4 -> 1.2.3] - withr [repo: RSPM -> CRAN; ver: 3.0.0 -> 2.5.0] - xfun [repo: RSPM -> CRAN; ver: 0.46 -> 0.40] - yaml [repo: RSPM -> CRAN; ver: 2.3.10 -> 2.3.7] Do you want to proceed? [Y/n]: y - Removing pak [0.7.2] ... OK [removed from library] Installation of 'curl 5.0.2' was requested, but the following constraints are not met: - httr2 (requires curl >= 5.1.0) renv will try to install 'curl 5.2.1' instead. Installation of 'htmltools 0.5.6' was requested, but the following constraints are not met: - bslib (requires htmltools >= 0.5.8) renv will try to install 'htmltools 0.5.8.1' instead. Installation of 'sass 0.4.7' was requested, but the following constraints are not met: - bslib (requires sass >= 0.4.9) renv will try to install 'sass 0.4.9' instead. # Downloading packages ------------------------------------------------------- - Downloading sass from CRAN ... OK [2.9 Mb in 0.66s] Installation of 'highr 0.10' was requested, but the following constraints are not met: - knitr (requires highr >= 0.11) renv will try to install 'highr 0.11' instead. Installation of 'xfun 0.40' was requested, but the following constraints are not met: - knitr (requires xfun >= 0.44) renv will try to install 'xfun 0.46' instead. - Downloading xfun from CRAN ... OK [155.5 Kb in 0.19s] Successfully downloaded 2 packages in 1.1 seconds. # Installing packages -------------------------------------------------------- - Installing cli ... OK [copied local binary and cached] - Installing curl ... OK [linked from cache] - Installing glue ... OK [copied local binary and cached] - Installing lifecycle ... OK [copied local binary and cached] - Installing askpass ... OK [copied local binary and cached] - Installing openssl ... OK [copied local binary and cached] - Installing withr ... OK [copied local binary and cached] - Installing httr2 ... OK [copied local binary and cached] - Installing cpp11 ... OK [copied local binary and cached] - Installing systemfonts ... OK [copied local binary and cached] - Installing ps ... OK [copied local binary and cached] - Installing processx ... OK [copied local binary and cached] - Installing callr ... OK [copied local binary and cached] - Installing fastmap ... OK [copied local binary and cached] - Installing utf8 ... OK [copied local binary and cached] - Installing cachem ... OK [copied local binary and cached] - Installing digest ... OK [copied local binary and cached] - Installing htmltools ... OK [linked from cache] - Installing jsonlite ... OK [copied local binary and cached] - Installing fs ... OK [copied local binary and cached] - Installing sass ... OK [built from source and cached in 22s] - Installing bslib ... OK [copied local binary and cached in 0.34s] - Installing evaluate ... OK [copied local binary and cached] - Installing xfun ... OK [built from source and cached in 2.4s] - Installing highr ... OK [linked from cache] - Installing yaml ... OK [copied local binary and cached] - Installing knitr ... OK [copied local binary and cached] - Installing tinytex ... OK [copied local binary and cached] - Installing rmarkdown ... OK [copied local binary and cached in 0.15s] - Installing textshaping ... OK [copied local binary and cached] - Installing ragg ... OK [copied local binary and cached] - Installing brio ... OK [copied local binary and cached in 0.16s] - Installing desc ... OK [copied local binary and cached in 0.44s] - Installing fansi ... OK [copied local binary and cached] - Installing downlit ... OK [copied local binary and cached] - Installing pkgdown ... OK [copied local binary and cached in 0.45s] The dependency tree was repaired during package installation: - askpass [1.2.0] - brio [1.1.5] - bslib [0.7.0] - cachem [1.1.0] - callr [3.7.6] - cli [3.6.3] - cpp11 [0.4.7] - curl [5.2.1] - desc [1.4.3] - digest [0.6.36] - downlit [0.4.4] - evaluate [0.24.0] - fansi [1.0.6] - fastmap [1.2.0] - fs [1.6.4] - glue [1.7.0] - highr [0.11] - htmltools [0.5.8.1] - httr2 [1.0.2] - jsonlite [1.8.8] - knitr [1.48] - lifecycle [1.0.4] - openssl [2.2.0] - pkgdown [2.1.0] - processx [3.8.4] - ps [1.7.7] - ragg [1.3.2] - rmarkdown [2.27] - sass [0.4.9] - systemfonts [1.1.0] - textshaping [0.4.0] - tinytex [0.52] - utf8 [1.2.4] - withr [3.0.0] - xfun [0.46] - yaml [2.3.10] Call `renv::snapshot()` to capture these dependencies in the lockfile. > renv::status() The following package(s) are in an inconsistent state: package installed recorded used httr y y n The following package(s) are out of sync [lockfile != library]: # CRAN ----------------------------------------------------------------------- - sass [0.4.7 != 0.4.9] - xfun [0.40 != 0.46] # RSPM ----------------------------------------------------------------------- - askpass [repo: CRAN != RSPM; ver: 1.1 != 1.2.0] - brio [repo: CRAN != RSPM; ver: 1.1.3 != 1.1.5] - bslib [repo: CRAN != RSPM; ver: 0.5.1 != 0.7.0] - cachem [repo: CRAN != RSPM; ver: 1.0.8 != 1.1.0] - callr [repo: CRAN != RSPM; ver: 3.7.3 != 3.7.6] - cli [repo: CRAN != RSPM; ver: 3.6.1 != 3.6.3] - cpp11 [repo: CRAN != RSPM; ver: 0.4.6 != 0.4.7] - curl [repo: CRAN != RSPM; ver: 5.0.2 != 5.2.1] - desc [repo: CRAN != RSPM; ver: 1.4.2 != 1.4.3] - digest [repo: CRAN != RSPM; ver: 0.6.33 != 0.6.36] - downlit [repo: CRAN != RSPM; ver: 0.4.3 != 0.4.4] - evaluate [repo: CRAN != RSPM; ver: 0.22 != 0.24.0] - fansi [repo: CRAN != RSPM; ver: 1.0.4 != 1.0.6] - fastmap [repo: CRAN != RSPM; ver: 1.1.1 != 1.2.0] - fs [repo: CRAN != RSPM; ver: 1.6.3 != 1.6.4] - glue [repo: CRAN != RSPM; ver: 1.6.2 != 1.7.0] - highr [repo: CRAN != RSPM; ver: 0.10 != 0.11] - htmltools [repo: CRAN != RSPM; ver: 0.5.6 != 0.5.8.1] - httr2 [repo: CRAN != RSPM; ver: 0.2.3 != 1.0.2] - jsonlite [repo: CRAN != RSPM; ver: 1.8.7 != 1.8.8] - knitr [repo: CRAN != RSPM; ver: 1.44 != 1.48] - lifecycle [repo: CRAN != RSPM; ver: 1.0.3 != 1.0.4] - openssl [repo: CRAN != RSPM; ver: 2.0.6 != 2.2.0] - pkgdown [repo: CRAN != RSPM; ver: 2.0.7 != 2.1.0] - processx [repo: CRAN != RSPM; ver: 3.8.2 != 3.8.4] - ps [repo: CRAN != RSPM; ver: 1.7.5 != 1.7.7] - ragg [repo: CRAN != RSPM; ver: 1.2.5 != 1.3.2] - rmarkdown [repo: CRAN != RSPM; ver: 2.25 != 2.27] - systemfonts [repo: CRAN != RSPM; ver: 1.0.5 != 1.1.0] - textshaping [repo: CRAN != RSPM; ver: 0.3.7 != 0.4.0] - tinytex [repo: CRAN != RSPM; ver: 0.47 != 0.52] - utf8 [repo: CRAN != RSPM; ver: 1.2.3 != 1.2.4] - withr [repo: CRAN != RSPM; ver: 2.5.0 != 3.0.0] - yaml [repo: CRAN != RSPM; ver: 2.3.7 != 2.3.10] See ?renv::status() for advice on resolving these issues. ```

I guess the reason for this is explained by the messages during installation (“Installation of 'PKG VERSION' was requested, but the following constraints are not met: […] renv will try to install 'PKG OTHE_VERSION' instead.”) but it’s not clear why this happens, since the previously snapshotted state of the library was internally consistent.

[klmr]

Hm. Actually from the output of renv::status() it looks like renv::restore() didn’t actually do… anything?!

I tried the same using the dev version of ‘renv’, with the same result.

[kevinushey]

This sounds similar to a recent issue where renv's dependency repair seemed to malfunction when the restore would act upon a library path that already contained differing versions of packages...

For diagnostics, does the issue still occur if you restore into a separate library path, e.g. something like:

renv::restore(library = "/tmp/renv-library")

Or alternatively, attempt the restore only after cleaning up the library paths?

(This might be suitable as a workaround, but even so it seems like there's definitely a bug in renv that needs to be fixed.)

[kevinushey]

Could you also share a couple of files?

• The lockfile you're using for renv::restore();
• The current state of your library paths, as via e.g. renv::snapshot(lockfile = "renv-current.lock")

This should let me try and reproduce from a similar state as from what you're working with.

[klmr]

Okay, I tried restoring into a separate library path, and I originally got the same behaviour as when disabling ‘pak’ above: it restores everything, but afterwards renv::status() still showed the mismatching versions — identical output as above. But then I remembered that .libPaths() wasn’t adjusted, and once I added the temporary library path to .libPaths(), renv::status() showed me a consistent state.

Maybe that’s a hint at what’s going wrong? I.e. that renv::restore() might somehow be using an incorrect library path? (I did check the library by stepping through renv::restore, and it corresponds to the value of .libPaths()[1], as expected.)

(At this point I should also note that renv::status() is in fact showing the correct status: I have manually verified that the package versions in the library and in the lockfile were as shown; so the error isn’t in renv::status().)

I’ve attached the requested files. Unfortunately the project is relatively complex. I can try to simplify it if absolutely necessary. I’ll also list my ‘renv’ config below. I’ve censored some company specifics. All censored CRAN-like repo URIs lead to valid PPM instances (I tested them just now to be sure).

‘renv’ config

``` > lapply(renv::config, \(f) f()) |> structure(class = 'simple.list') _ activate.prompt TRUE autoloader.enabled TRUE auto.snapshot FALSE bitbucket.host api.bitbucket.org/2.0 copy.method auto connect.timeout 20 connect.retry 3 cache.enabled TRUE cache.symlinks TRUE dependency.errors reported dependencies.limit 1000 exported.functions * external.libraries /Users/USER/Library/Application Support/R/nvimcom/%p-library/%v filebacked.cache TRUE github.host api.github.com gitlab.host gitlab.com install.build FALSE install.remotes TRUE install.shortcuts TRUE install.staged TRUE install.transactional TRUE install.verbose FALSE locking.enabled FALSE mran.enabled FALSE pak.enabled TRUE ppm.enabled TRUE ppm.default TRUE ppm.url https://packagemanager.posit.co/cran/latest rspm.enabled TRUE sandbox.enabled TRUE shims.enabled TRUE snapshot.inference TRUE snapshot.validate TRUE synchronized.check TRUE updates.check FALSE updates.parallel 2 user.environ TRUE user.library FALSE user.profile FALSE ``` And the paths: ``` > lapply(renv::config, \(f) f()) |> structure(class = 'simple.list') _ root /Users/USER/Library/Caches/R/renv library /Users/USER/Library/Application Support/R/renv/bigbrother-1cca52a8/R-4.3/aarch64-apple-darwin20 lockfile /Users/USER/Code/bigbrother/renv.lock settings renv/settings.json cache /Users/USER/Library/Caches/R/renv/cache/v5/R-4.3/aarch64-apple-darwin20 sandbox /Users/USER/Library/Caches/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659 ```

🗜️ renv-lockfiles.zip

[kevinushey]

Darn -- even trying to replicate a restore using the same set of packages as in your case, I'm not able to reproduce. 😞

Based on the error, my suspicion is that something is going wrong when computing and adding the requirements for each package during restore here:

https://github.com/rstudio/renv/blob/6d8045719b34787506f0a541f9ebd56161988add/R/retrieve.R#L1052-L1064

Perhaps renv_dependencies_discover_description() is returning the wrong value here for some reason; e.g. using the version of a package currently-loaded or available in the library paths, as opposed to the version that was just downloaded?

A couple other options you could try setting, before attempting restore:

# disable internal caching / memoization of computed values
options(renv.dynamic.enabled = FALSE)

# disable caching of values computed from files on disk
options(renv.config.filebacked.cache = FALSE)

If either of these help, it could help narrow down the issue as well.

[Fuco1]

I'm using version 1.0.8 and with pak I also get incorrect versions installed. All the versions in the library are newer which leads me to believe pack simply grabs whatever is the latest version at the moment.

I tried it now with pak disable and with the two options you provided and the result is the same.

# CRAN -----------------------------------------------------------------------
- broom            [1.0.5 != 1.0.6]
- colorspace       [2.1-0 != 2.1-1]
- data.table       [1.15.4 != 1.16.0]
- DBI              [1.2.2 != 1.2.3]
- distributional   [0.4.0 != 0.5.0]
- fabletools       [0.4.2 != 0.5.0]
- feasts           [0.3.2 != 0.4.0]
- filelock         [r-lib/filelock != 1.0.3]
- ggnewscale       [0.4.10 != 0.5.0]
- jsonlite         [1.8.8 != 1.8.9]
- odbc             [1.4.2 != 1.5.0]
- openssl          [2.1.2 != 2.2.2]
- rlang            [1.1.3 != 1.1.4]
- tsibble          [1.1.4 != 1.1.5]
- urca             [1.3-3 != 1.3-4]
- yaml             [2.3.8 != 2.3.10]

I guess the theory that it is trying to bump versions to get a resolvable set might be correct. But I don't know which package might be causing the problem and also... that should rather produce an error.