I have some script written using R programming language, and for my friends to run those scripts in their own machines without any problems and so that they can get same environment variable as me, I shared with them the renv.lock, .Rprofile, and renv/activate.R files.
However, they are facing some issues in getting the dependencies installed in their pcs. What they did first was set the working directory to the specific project folder, and then run the following commands respectively:
renv::restore()
renv::install()
And in doing so they are getting the following error:
renv::restore()
It looks like you've called renv::restore() in a project that hasn't been activated yet.
How would you like to proceed?
1: Activate the project and use the project library.
2: Do not activate the project and use the current library paths.
3: Cancel and resolve the situation another way.
Selection: 1
Restarting R session...
- Project 'C:/Users/Lenovo/Desktop/RProjects/the_app' loaded. [renv 1.0.3]
- None of the packages recorded in the lockfile are currently installed.
> renv::install()
- Unrecognized response: please enter 'y' or 'n', or type Ctrl + C to cancel.
- Would you like to restore the project library? [y/N]: y
The following package(s) will be updated:
# CRAN -----------------------------------------------------------------------
- base64enc [* -> 0.1-3]
- bslib [* -> 0.5.1]
- cachem [* -> 1.0.8]
- cli [* -> 3.6.1]
- commonmark [* -> 1.9.0]
- crayon [* -> 1.5.2]
- digest [* -> 0.6.33]
- ellipsis [* -> 0.3.2]
- fastmap [* -> 1.1.1]
- fontawesome [* -> 0.5.2]
- fresh [* -> 0.2.0]
- fs [* -> 1.6.3]
- glue [* -> 1.6.2]
- gridExtra [* -> 2.3]
- gtable [* -> 0.3.4]
- htmltools [* -> 0.5.6.1]
- httpuv [* -> 1.6.11]
- jquerylib [* -> 0.1.4]
- jsonlite [* -> 1.8.7]
- later [* -> 1.3.1]
- lifecycle [* -> 1.0.3]
- magrittr [* -> 2.0.3]
- memoise [* -> 2.0.1]
- mime [* -> 0.12]
- png [* -> 0.1-8]
- promises [* -> 1.2.1]
- R6 [* -> 2.5.1]
- rappdirs [* -> 0.3.3]
- Rcpp [* -> 1.0.11]
- rlang [* -> 1.1.1]
- rstudioapi [* -> 0.15.0]
- sass [* -> 0.4.7]
- shiny [* -> 1.7.5]
- shinydashboard [* -> 0.7.2]
- sourcetools [* -> 0.1.7-1]
- withr [* -> 2.5.1]
- xtable [* -> 1.8-4]
# Downloading packages -------------------------------------------------------
- Querying repositories for available binary packages ... Done!
renv was unable to query available packages from the following repositories:
- # https://packagemanager.posit.co/cran/latest/bin/windows/contrib/4.3 --------
error downloading 'https://packagemanager.posit.co/cran/latest/bin/windows/contrib/4.3/PACKAGES.rds' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
error downloading 'https://packagemanager.posit.co/cran/latest/bin/windows/contrib/4.3/PACKAGES.gz' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
error downloading 'https://packagemanager.posit.co/cran/latest/bin/windows/contrib/4.3/PACKAGES' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
- Querying repositories for available source packages ... Done!
renv was unable to query available packages from the following repositories:
- # https://packagemanager.posit.co/cran/latest/src/contrib --------------------
error downloading 'https://packagemanager.posit.co/cran/latest/src/contrib/PACKAGES.rds' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
error downloading 'https://packagemanager.posit.co/cran/latest/src/contrib/PACKAGES.gz' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
error downloading 'https://packagemanager.posit.co/cran/latest/src/contrib/PACKAGES' [curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.]
Warning: failed to find binary for 'htmltools 0.5.6.1' in package repositories
Warning: failed to find source for 'htmltools 0.5.6.1' in package repositories
Error: failed to retrieve package 'htmltools@0.5.6.1'
Traceback (most recent calls last):
31: source("renv/activate.R")
30: withVisible(eval(ei, envir))
29: eval(ei, envir)
28: eval(ei, envir)
27: local(...) at activate.R#2
26: eval.parent(substitute(eval(quote(expr), envir)))
25: eval(expr, p)
24: eval(expr, p)
23: eval(quote(...), new.env())
22: eval(quote(...), new.env())
21: renv_bootstrap_exec(project, libpath, version) at activate.R#1176
20: if (!renv_bootstrap_load(project, libpath, version))
renv_bootstrap_run(version, libpath) at activate.R#1009
19: renv::load(project) at activate.R#864
18: renv_load_finish(project, lockfile)
17: renv_load_report_synchronized(project, lockfile)
16: restore(project, prompt = FALSE, exclude = "renv")
15: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
14: retrieve(packages)
13: handler(package, renv_retrieve_impl(package))
12: renv_retrieve_impl(package)
11: renv_retrieve_successful(record, path)
10: (function() {
repos <- if (is.null(desc$biocViews))
getOption("repos")
else renv_bioconductor_repos()
renv_scope_options(repos = repos)
renv_retrieve_successful_recurse(deps)
})()
9: renv_retrieve_successful_recurse(deps)
8: renv_retrieve_successful_recurse_impl(remote)
7: dynamic(key = list(remote = remote), value = renv_retrieve_successful_recurse_impl_one(remote))
6: the$dynamic_objects[[id]] %||% {
dlog("dynamic", "memoizing dynamic value for '%s'", id)
value
}
5: renv_retrieve_successful_recurse_impl_one(remote)
4: renv_retrieve_impl(remote)
3: renv_retrieve_repos(record)
2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
1: stop(sprintf(fmt, ...), call. = call.)
They then run the renv::diagnostics() command and the following is what they got:
> renv::diagnostics()
Diagnostics Report [renv 1.0.3]
===============================
# Session Info ---------------------------------------------------------------
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics datasets grDevices utils methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1 renv_1.0.3
# Project --------------------------------------------------------------------
Project path: "C:/Users/Lenovo/Desktop/RProjects/the_app"
# Status ---------------------------------------------------------------------
The following package(s) are missing:
package installed recorded used
base64enc n y ?
bslib n y ?
cachem n y ?
cli n y ?
commonmark n y ?
crayon n y ?
digest n y ?
ellipsis n y ?
fastmap n y ?
fontawesome n y ?
fresh n y y
fs n y ?
glue n y ?
gridExtra n y y
gtable n y ?
htmltools n y ?
httpuv n y ?
jquerylib n y ?
jsonlite n y y
later n y ?
lifecycle n y ?
magrittr n y ?
memoise n y ?
mime n y ?
png n y y
promises n y ?
R6 n y ?
rappdirs n y ?
Rcpp n y ?
rlang n y ?
rstudioapi n y ?
sass n y ?
shiny n y y
shinydashboard n y y
sourcetools n y ?
withr n y ?
xtable n y ?
See ?renv::status() for advice on resolving these issues.
# Packages -------------------------------------------------------------------
Library Source Lockfile Source Path Dependency
KernSmooth 2.23-21 CRAN <NA> <NA> [2] <NA>
MASS 7.3-60 CRAN <NA> <NA> [2] <NA>
Matrix 1.5-4.1 CRAN <NA> <NA> [2] <NA>
R6 <NA> <NA> 2.5.1 CRAN <NA> <NA>
Rcpp <NA> <NA> 1.0.11 CRAN <NA> <NA>
base <NA> <NA> <NA> <NA> [2] direct
base64enc <NA> <NA> 0.1-3 CRAN <NA> <NA>
boot 1.3-28.1 CRAN <NA> <NA> [2] <NA>
bslib <NA> <NA> 0.5.1 CRAN <NA> <NA>
cachem <NA> <NA> 1.0.8 CRAN <NA> <NA>
class 7.3-22 CRAN <NA> <NA> [2] <NA>
cli <NA> <NA> 3.6.1 CRAN <NA> <NA>
cluster 2.1.4 CRAN <NA> <NA> [2] <NA>
codetools 0.2-19 CRAN <NA> <NA> [2] <NA>
commonmark <NA> <NA> 1.9.0 CRAN <NA> <NA>
crayon <NA> <NA> 1.5.2 CRAN <NA> <NA>
digest <NA> <NA> 0.6.33 CRAN <NA> <NA>
ellipsis <NA> <NA> 0.3.2 CRAN <NA> <NA>
fastmap <NA> <NA> 1.1.1 CRAN <NA> <NA>
fontawesome <NA> <NA> 0.5.2 CRAN <NA> <NA>
foreign 0.8-84 CRAN <NA> <NA> [2] <NA>
fresh <NA> <NA> 0.2.0 CRAN <NA> direct
fs <NA> <NA> 1.6.3 CRAN <NA> <NA>
glue <NA> <NA> 1.6.2 CRAN <NA> <NA>
grDevices <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] direct
gridExtra <NA> <NA> 2.3 CRAN <NA> direct
gtable <NA> <NA> 0.3.4 CRAN <NA> <NA>
htmltools <NA> <NA> 0.5.6.1 CRAN <NA> <NA>
httpuv <NA> <NA> 1.6.11 CRAN <NA> <NA>
jquerylib <NA> <NA> 0.1.4 CRAN <NA> <NA>
jsonlite <NA> <NA> 1.8.7 CRAN <NA> direct
later <NA> <NA> 1.3.1 CRAN <NA> <NA>
lattice 0.21-8 CRAN <NA> <NA> [2] <NA>
lifecycle <NA> <NA> 1.0.3 CRAN <NA> <NA>
magrittr <NA> <NA> 2.0.3 CRAN <NA> <NA>
memoise <NA> <NA> 2.0.1 CRAN <NA> <NA>
mgcv 1.8-42 CRAN <NA> <NA> [2] <NA>
mime <NA> <NA> 0.12 CRAN <NA> <NA>
nlme 3.1-162 CRAN <NA> <NA> [2] <NA>
nnet 7.3-19 CRAN <NA> <NA> [2] <NA>
png <NA> <NA> 0.1-8 CRAN <NA> direct
promises <NA> <NA> 1.2.1 CRAN <NA> <NA>
rappdirs <NA> <NA> 0.3.3 CRAN <NA> <NA>
renv 1.0.3 CRAN 1.0.3 CRAN [1] direct
rlang <NA> <NA> 1.1.1 CRAN <NA> <NA>
rpart 4.1.19 CRAN <NA> <NA> [2] <NA>
rstudioapi <NA> <NA> 0.15.0 CRAN <NA> <NA>
sass <NA> <NA> 0.4.7 CRAN <NA> <NA>
shiny <NA> <NA> 1.7.5 CRAN <NA> direct
shinydashboard <NA> <NA> 0.7.2 CRAN <NA> direct
sourcetools <NA> <NA> 0.1.7-1 CRAN <NA> <NA>
spatial 7.3-16 CRAN <NA> <NA> [2] <NA>
survival 3.5-5 CRAN <NA> <NA> [2] <NA>
tools <NA> <NA> <NA> <NA> [2] direct
utils <NA> <NA> <NA> <NA> [2] direct
withr <NA> <NA> 2.5.1 CRAN <NA> <NA>
xtable <NA> <NA> 1.8-4 CRAN <NA> <NA>
[1]: C:/Users/Lenovo/Desktop/RProjects/the_app/renv/library/R-4.3/x86_64-w64-mingw32
[2]: C:/Users/Lenovo/AppData/Local/R/cache/R/renv/sandbox/R-4.3/x86_64-w64-mingw32/bd3f13aa
# ABI ------------------------------------------------------------------------
- ABI conflict checks are not yet implemented on Windows.
# 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 8
$ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
$ download.file.method : chr "libcurl"
$ download.file.extra : NULL
$ install.packages.compile.from.source: chr "interactive"
$ pkgType : chr "both"
$ repos : Named chr "https://packagemanager.posit.co/cran/latest"
..- attr(*, "names")= chr "CRAN"
$ renv.consent : logi TRUE
$ renv.verbose : logi TRUE
# Environment Variables ------------------------------------------------------
HOME = C:\Users\Lenovo\Documents
LANG = <NA>
MAKE = <NA>
R_LIBS = <NA>
R_LIBS_SITE = C:/PROGRA~1/R/R-43~1.1/site-library
R_LIBS_USER = C:/Users/Lenovo/Desktop/RProjects/the_app/renv/library/R-4.3/x86_64-w64-mingw32
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = C:/PROGRA~1/R/R-43~1.1/site-library
RENV_DEFAULT_R_LIBS_USER = C:\Users\Lenovo\AppData\Local/R/win-library/4.3
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = C:/Users/Lenovo/Desktop/RProjects/the_app
# PATH -----------------------------------------------------------------------
- C:\Users\Lenovo\OriPrograms\Scripts
- C:\Users\Lenovo\OriPrograms
- c:\rtools43\x86_64-w64-mingw32.static.posix\bin
- c:\rtools43\usr\bin
- C:\Program Files\R\R-4.3.1\bin\x64
- C:\Program Files\R\R-4.3.1\bin\x64
- C:\Program Files (x86)\VMware\VMware Player\bin\
- C:\Program Files (x86)\Common Files\Oracle\Java\javapath
- C:\php
- C:\Program Files\MiKTeX 2.9\miktex\bin\x64\
- C:\Program Files\Git\cmd
- C:\Program Files\PostgreSQL\14\bin
- C:\Program Files\PostgreSQL\14\lib
- C:\Program Files\Google\Google Apps Migration\
- C:\Users\Lenovo\anaconda3\Library\bin
- C:\Python36-32
- C:\Python36-32\Lib\site-packages
- C:\Python36-32\Scripts
- C:\Users\Lenovo\OriPrograms\Microsoft VS Code\bin
- C:\Users\Lenovo\anaconda3\Scripts
- C:\Program Files\RStudio\resources\app\bin\quarto\bin
- C:\Program Files\RStudio\resources\app\bin\postback
# Cache ----------------------------------------------------------------------
There are a total of 37 packages installed in the renv cache.
Cache path: "C:/Users/Lenovo/AppData/Local/R/cache/R/renv/cache/v5/R-4.3/x86_64-w64-mingw32"
My question is how can we resolve this problem? Any advice is much appreciated.
So, as suggested in the comments, this problem was solved by first creating .Renviron file in the project directory, and then and adding the following line to that file (.Renviron):
Sys.setenv(RENV_DOWNLOAD_METHOD = getOption("download.file.method"))
and saving it.