Cannot install Hmisc using renv: Installing Formula [1.2-4] ... FAILED

Question

when trying to install Hmisc in R using renv I get the message underneath. Could somebody help me please?

I'm using:

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics", with
RStudio 2022.02.3 Build 492, using a 
Platform: x86_64-apple-darwin17.0 (64-bit), and  
renv 0.14.0

--

Installing 'Hmisc' ...
[1/6] Installing Formula...
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.2/Formula_1.2-4.tgz' ...
    OK [file is up to date]
Installing Formula [1.2-4] ...
    FAILED

Error in if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :  the condition has length > 1

Calls: sourceWithProgress ... renv_scope_install -> renv_scope_install_macos -> case

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 1
Traceback (most recent calls last):

15: sourceWithProgress(script = "/var/folders/y9/8c6qs4hj6pq1nnv725g7gbxw0000gn/T/9878-ce12-709e-35eb", 
        encoding = "UTF-8", con = stdout(), importRdata = NULL, exportRdata = NULL)

14: eval(statements[[idx]], envir = sourceEnv)

13: eval(statements[[idx]], envir = sourceEnv)

12: renv::install("Formula")

11: renv_install_impl(records)

10: renv_install_staged(records)

 9: renv_install_default(records)

 8: handler(package, renv_install_package(record))

 7: renv_install_package(record)

 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })

 5: renv_install_package_impl(record)

 4: r_cmd_install(package, path)

 3: renv_scope_install()

 2: renv_scope_install_macos(.envir)

 1: case(matches("/usr/bin/clang") ~ TRUE, matches("clang") ~ Sys.which("clang") == 
        "/usr/bin/clang", FALSE)

Execution halted

Can you please share the output of `system2(renv:::R(), "CMD config CC")`? It seems like R is reporting the C compiler used by your R installation in a way that `renv` is not expecting. — Kevin Ushey, Jun 09 '22 at 20:52
If you recently updated macOS, you might also need to reinstall command line tools. Use `xcode-select --install` from the command line to re-install them. — Kevin Ushey, Jun 11 '22 at 03:27
thanks for answering, here is the report from: system2(renv:::R(), "CMD config CC"): clang -mmacosx-version-min=10.13. Indeed, I recently updated my Macbook. I run xcode-select --install and then tried to install 'Hmisc' again and now it works! thanks you so much! — menarest, Jun 13 '22 at 10:55

score 1 · Accepted Answer · answered Jun 13 '22 at 18:33

This part of the stack trace:

 < ... >
 3: renv_scope_install()

 2: renv_scope_install_macos(.envir)

 1: case(matches("/usr/bin/clang") ~ TRUE, matches("clang") ~ Sys.which("clang") == 
        "/usr/bin/clang", FALSE)

suggests that something went wrong when renv was trying to query information about the system compiler.

Somewhat surprisingly, whenever one upgrades to a new version of macOS, any existing command line tools (CLT) installation will be removed, and needs to be manually re-installed. renv relies on these command line tools being available when querying information about the system's installation capabilities, so re-installing command line tools with:

xcode-select --install

should alleviate the issue.

I've also made some changes in the development version of renv to ensure that this situation is handled and reported better.

Cannot install Hmisc using renv: Installing Formula [1.2-4] ... FAILED

1 Answers1