renv fails on install.packages() and restore() - r

Question

In both new (dummy) packages and mature packages with renv already initialized, renv fails on install.packages() and restore().
Note: to avoid tripping the spam filter, I've replaced all instances of 'https://' with 'web.'
Failure on install.packages(), with, e.g., dplyr:
> install.packages("dplyr")
Retrieving 'web.cloud.r-project.org/bin/macosx/contrib/4.2/dplyr_1.1.0.tgz' ...
OK [downloaded 1.5 Mb in 0.4 secs]
Retrieving 'web.cloud.r-project.org/bin/macosx/contrib/4.2/cli_3.6.0.tgz' ...
OK [file is up to date]
[...]
Retrieving 'web.cloud.r-project.org/bin/macosx/contrib/4.2/withr_2.5.0.tgz' ...
OK [file is up to date]
Installing cli [3.6.0] ...
FAILED
Error in if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1
In addition: Warning message:
In system2(R(), args, stdout = TRUE, stderr = TRUE) :
running command ''/Library/Frameworks/R.framework/Resources/bin/R' CMD config CC 2>&1' had status 71
Failure on renv::restore():
> renv::restore()
The following package(s) will be updated:
# CRAN ===============================
- KernSmooth [2.23-20 -> 2.23-18]
- MASS [7.3-58.2 -> 7.3-53.1]
[...]
- zip [* -> 2.2.2]
# GitHub =============================
- staged.dependencies [* -> remoteproject/staged.dependencies#HEAD]
Do you want to proceed? [y/N]: y
* Querying repositories for available binary packages ... Done!
* Querying repositories for available source packages ... Done!
Retrieving 'web.cran.microsoft.com/snapshot/2021-03-31/src/contrib/boot_1.3-27.tar.gz' ...
OK [file is up to date]
Retrieving 'web.cran.microsoft.com/snapshot/2021-03-31/src/contrib/class_7.3-18.tar.gz' ...
OK [file is up to date]
[...]
Retrieving 'web.cran.microsoft.com/snapshot/2021-03-31/src/contrib/visNetwork_2.0.9.tar.gz' ...
OK [file is up to date]
Installing boot [1.3-27] ...
FAILED
Error in if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1
In addition: Warning messages:
1: could not retrieve available packages for url 'web.cran.microsoft.com/snapshot/2021-03-31/bin/macosx/contrib/4.2'
2: In system2(R(), args, stdout = TRUE, stderr = TRUE) :
running command ''/Library/Frameworks/R.framework/Resources/bin/R' CMD config CC 2>&1' had status 71
Session info:
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] MASS_7.3-58.2 compiler_4.2.1 tools_4.2.1 renv_0.16.0
Judging from answers here and in other forums, the following might be useful information:
Output from getOption("repos"):
> getOption("repos")
CRAN MRAN
"web.cloud.r-project.org" "web.cran.microsoft.com/snapshot/2021-03-31"
Output from installing directly from utils package:
> utils::install.packages("dplyr")
Installing package into ‘/Users/dlei/Library/Caches/org.R-project.R/R/renv/library/project-01109165/R-4.2/x86_64-apple-darwin17.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fansi’, ‘utf8’, ‘pkgconfig’, ‘withr’, ‘cli’, ‘generics’, ‘glue’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘R6’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘vctrs’
Warning: unable to access index for repository web.cran.microsoft.com/snapshot/2021-03-31/bin/macosx/contrib/4.2:
cannot open URL 'web.cran.microsoft.com/snapshot/2021-03-31/bin/macosx/contrib/4.2/PACKAGES'
trying URL 'web.cloud.r-project.org/bin/macosx/contrib/4.2/fansi_1.0.4.tgz'
Content type 'application/x-gzip' length 364195 bytes (355 KB)
==================================================
downloaded 355 KB
trying URL 'web.cloud.r-project.org/bin/macosx/contrib/4.2/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196823 bytes (192 KB)
==================================================
downloaded 192 KB
[...]
The downloaded binary packages are in
/var/folders/41/y38m8sw12871hpn_5nl9y88m0000gn/T//RtmpIwcHeu/downloaded_packages
Output from renv::diagnostics():
> renv::diagnostics()
Diagnostics Report [renv 0.16.0]
================================
# Session Info =======================
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] MASS_7.3-58.2 compiler_4.2.1 tools_4.2.1 renv_0.16.0
# Project ============================
Project path: "~/Desktop/Git_Repos/project"
# Status =============================
The following package(s) do not appear to be used in this project:
_
BH [1.75.0-0]
KernSmooth [2.23-18]
[...]
zip [2.2.2]
Use `renv::snapshot()` to remove them from the lockfile.
The following package(s) are recorded in the lockfile, but not installed:
_
DT [0.17]
covr [3.5.1]
[...]
staged.dependencies [remoteproject/staged.dependencies#HEAD]
usethis [2.1.6]
Use `renv::restore()` to install these packages.
The following package(s) are out of sync:
Package Lockfile Version Library Version
R6 2.5.0 2.5.1
cli 3.4.1 3.6.0
[...]
vctrs 0.5.0 0.5.2
Use `renv::snapshot()` to save the state of your library to the lockfile.
Use `renv::restore()` to restore your library from the lockfile.
The following package(s) are used in the project, but are not installed:
project.test
projectdev
Consider installing these packages, and then using `renv::snapshot()`
to record these packages in the lockfile.
# Packages ===========================
Library Source Lockfile Source Path Dependency
BH <NA> <NA> 1.75.0-0 CRAN <NA> <NA>
DT <NA> <NA> 0.17 CRAN <NA> direct
[...]
zip <NA> <NA> 2.2.2 CRAN <NA> <NA>
[1]: /Users/dlei/Library/Caches/org.R-project.R/R/renv/library/project-01109165/R-4.2/x86_64-apple-darwin17.0
[2]: /Users/dlei/Desktop/Git_Repos/project/renv/sandbox/R-4.2/x86_64-apple-darwin17.0/84ba8b13
# ABI ================================
* No ABI conflicts were detected in the set of installed packages.
# User Profile =======================
[no user profile detected]
# 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 9
$ 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 [1:2] "web.cloud.r-project.org" "web.cran.microsoft.com/snapshot/2021-03-31"
..- attr(*, "names")= chr [1:2] "CRAN" "MRAN"
$ renv.consent : logi TRUE
$ renv.project.path : chr "/Users/dlei/Desktop/Git_Repos/project"
$ renv.verbose : logi TRUE
# Environment Variables ==============
HOME = /Users/dlei
LANG = en_CA.UTF-8
MAKE = make
R_LIBS = <NA>
R_LIBS_SITE = /Library/Frameworks/R.framework/Resources/site-library
R_LIBS_USER = /Users/dlei/Library/Caches/org.R-project.R/R/renv/library/project-01109165/R-4.2/x86_64-apple-darwin17.0:/Users/dlei/Desktop/Git_Repos/project/renv/sandbox/R-4.2/x86_64-apple-darwin17.0/84ba8b13
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = /Library/Frameworks/R.framework/Resources/site-library
RENV_DEFAULT_R_LIBS_USER = /Users/dlei/Library/R/x86_64/4.2/library
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = /Users/dlei/Desktop/Git_Repos/project
# PATH ===============================
- /usr/local/bin
- /usr/bin
- /bin
- /usr/sbin
- /sbin
- /Library/TeX/texbin
-
- /Applications/RStudio.app/Contents/MacOS/postback
# Cache ==============================
There are a total of 0 package(s) installed in the renv cache.
Cache path: "~/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.2/x86_64-apple-darwin17.0"
Output of getOption("download.file.method"):
> getOption("download.file.method")
[1] "libcurl"
Output of renv:::renv_download_method():
> renv:::renv_download_method()
[1] "curl"
As per recommendation in the RStudio community forum, I've tried setting renv's download method from curl to libcurl, but get a similar error:
> install.packages("dplyr")
Retrieving 'web.cloud.r-project.org/bin/macosx/contrib/4.2/dplyr_1.1.0.tgz' ...
OK [downloaded 1.5 Mb in 0.3 secs]
Installing dplyr [1.1.0] ...
FAILED
Error in if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1
In addition: Warning messages:
1: could not retrieve available packages for url 'web.cran.microsoft.com/snapshot/2021-03-31/bin/macosx/contrib/4.2'
2: In system2(R(), args, stdout = TRUE, stderr = TRUE) :
running command ''/Library/Frameworks/R.framework/Resources/bin/R' CMD config CC 2>&1' had status 71

Answer 1

Given this output in the error message:
Error in if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1
In addition: Warning message:
In system2(R(), args, stdout = TRUE, stderr = TRUE) :
running command ''/Library/Frameworks/R.framework/Resources/bin/R' CMD config CC 2>&1' had status 71
Did you recently update macOS on your machine? This looks like an issue in renv where attempts to query the current compiler could fail.
If so, I believe you can work around this by running:
xcode-select --install
from a terminal.

Answer 2

The links which were failing were cran snapshots with no corresponding url. Explicitly pointing to the CRAN repo by running restore(repos="https://cloud.r-project.org") solved this issue.
This issue was solved thanks to #nirgrahamuk in the community.rstudio forum (for those interested in the original answer, see here).