Warning messages on load after upgrading to renv 1.0.0

[mgriffiths2]

I was using renv 0.17.3 with no problem, then upgraded to 1.0.0 using renv::upgrade()

Now whenever I open my project, or run renv::load() I get a list of warning messages:

- Project '<project name>' loaded. [renv 1.0.0]
Warning messages:
1: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
2: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1
3: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
4: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1
5: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
6: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1
7: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
8: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1
9: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
10: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1

It still seems to work fine, but it would be nice to get rid of the warnings.

[kevinushey]

Do you get more detail if you use:

options(error = renv:::renv_error_handler_call())
options(warn = 2L)

Perhaps by putting this in your project's .Rprofile before source("renv/activate.R") is run?

[kevinushey]

A reproducible example would also help; e.g. if you could share your project sources publicly (e.g. on GitHub).

[mgriffiths2]

Unfortunately I'm not able to share the whole project. Would the renv lockfile help?

Here is what I get when I load with the options you suggested above:

Error in is.na(value) : 
  (converted from warning) (converted from warning) is.na() applied to non-(list or vector) of type 'language'
Traceback (most recent calls last):
35: source("renv/activate.R")
34: withVisible(eval(ei, envir))
33: eval(ei, envir)
32: eval(ei, envir)
31: local(...) at activate.R#2
30: eval.parent(substitute(eval(quote(expr), envir)))
29: eval(expr, p)
28: eval(expr, p)
27: eval(quote(...), new.env())
26: eval(quote(...), new.env())
25: if (renv_bootstrap_load(project, libpath, version))
      return(TRUE) at activate.R#1159
24: renv::load(project) at activate.R#847
23: renv_load_finish(project, lockfile)
22: renv_load_report_synchronized(project, lockfile)
21: (function() {
        renv_scope_options(renv.verbose = FALSE)
        status(project = project, sources = FALSE)
    })()
20: status(project = project, sources = FALSE)
19: renv_status_impl(project, libpaths, lockpath, sources, cache)
18: renv_snapshot_dependencies(project, dev = FALSE)
17: dynamic(list(project = project, type = type, dev = dev), renv_snapshot_dependencies_impl(project, 
        type, dev))
16: the$dynamic_objects[[id]] %||% {
        dlog("dynamic", "memoizing dynamic value for '%s'", id)
        value
    }
15: renv_snapshot_dependencies_impl(project, type, dev)
14: withCallingHandlers(renv_dependencies_impl(path = path, root = project, 
        field = "Package", errors = config$dependency.errors(), dev = dev), 
        renv.dependencies.problems = function(cnd) {
            if (identical(config$dependency.errors(), "ignored")) 
                return()
            if (interactive() && !proceed()) 
                cancel()
        }, renv.dependencies.elapsed_time = function(cnd) {
            if (!type %in% c("packrat", "implicit")) 
                return()
            elapsed <- cnd$data
            limit <- getOption("renv.dependencies.elapsed_time_threshold", 
                default = 10L)
            if (elapsed < limit) 
                return()
            lines <- c("", "NOTE: Dependency discovery took %s during snapshot.", 
                "Consider using .renvignore to ignore files, or switching to explicit snapshots.", 
                "See `?renv::dependencies` for more information.", 
                "")
            writef(lines, renv_difftime_format(elapsed))
        })
13: renv_dependencies_impl(path = path, root = project, field = "Package", 
        errors = config$dependency.errors(), dev = dev)
12: renv_dependencies_discover(files, progress, errors)
11: bapply(paths, renv_dependencies_discover_impl)
10: lapply(x, f, ...)
 9: FUN(X[[i]], ...)
 8: tryCatch(filebacked("dependencies", path, callback), error = function(cnd) {
        warning(cnd)
        NULL
    })
 7: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: value[[3L]](cond)
 4: warning(cnd)
 3: withRestarts({
        .Internal(.signalCondition(cond, message, call))
        .Internal(.dfltWarn(message, call))
    }, muffleWarning = function() NULL)
 2: withOneRestart(expr, restarts[[1L]])
 1: doWithOneRestart(return(expr), restart)

[nopsybot]

Hi, I also ran into warnings using 'renv::upgrade()' to migrate from 0.17.3 to 1.0.0 as an initial installation of the new version. I can't clarify the issue, but got a quick and dirty workaround:

1. remove renv package from project
2. close project
3. install new renv version (I did with install.packages())
4. run renv::activate(project = "your/r-project/to/upgrade")
5. when entering the project, follow the interactive instructions to record the new renv version in the lockfile

Anyway, thank you for the renv update!

[mgriffiths2]

It seems the error is occurring during dependency-finding:

Finding R package dependencies ... [104/123] Error in is.na(value) : (converted from warning) (converted from warning) is.na() applied to non-(list or vector) of type 'language'

[mgriffiths2]

I have now worked around this by specifying my dependencies explicitly in a DESCRIPTION file. I guess the error comes from parsing our code when finding dependencies.

[franzbischoff]

Here is my output:

- Project '/xxxxx/xxxxx' loaded. [renv 1.0.0]
Error in is.na(value) : 
  (converted from warning) (converted from warning) is.na() applied to non-(list or vector) of type 'language'
Traceback (most recent calls last):
46: local({
        try_source <- function(file) {
            if (file.exists(file)) {
                source(file)
                TRUE
            }
            else {
                FALSE
            }
        }
        r_profile <- Sys.getenv("R_PROFILE_USER_OLD")
        Sys.setenv(R_PROFILE_USER_OLD = "", R_PROFILE_USER = r_profile)
        if (nzchar(r_profile)) {
            try_source(r_profile)
        }
        else {
            try_source(".Rprofile") || try_source(file.path("~", 
                ".Rprofile"))
        }
        invisible()
    })
45: eval.parent(substitute(eval(quote(expr), envir)))
44: eval(expr, p)
43: eval(expr, p)
42: eval(quote({
        try_source <- function(file) {
            if (file.exists(file)) {
                source(file)
                TRUE
            } else {
                FALSE
            }
        }
        r_profile <- Sys.getenv("R_PROFILE_USER_OLD")
        Sys.setenv(R_PROFILE_USER_OLD = "", R_PROFILE_USER = r_profile)
        if (nzchar(r_profile)) {
            try_source(r_profile)
        } else {
            try_source(".Rprofile") || try_source(file.path("~", 
                ".Rprofile"))
        }
        invisible()
    }), new.env())
41: eval(quote({
        try_source <- function(file) {
            if (file.exists(file)) {
                source(file)
                TRUE
            } else {
                FALSE
            }
        }
        r_profile <- Sys.getenv("R_PROFILE_USER_OLD")
        Sys.setenv(R_PROFILE_USER_OLD = "", R_PROFILE_USER = r_profile)
        if (nzchar(r_profile)) {
            try_source(r_profile)
        } else {
            try_source(".Rprofile") || try_source(file.path("~", 
                ".Rprofile"))
        }
        invisible()
    }), new.env())
40: try_source(".Rprofile")
39: source(file)
38: withVisible(eval(ei, envir))
37: eval(ei, envir)
36: eval(ei, envir)
35: source("renv/activate.R") at .Rprofile#11
34: withVisible(eval(ei, envir))
33: eval(ei, envir)
32: eval(ei, envir)
31: local(...) at activate.R#2
30: eval.parent(substitute(eval(quote(expr), envir)))
29: eval(expr, p)
28: eval(expr, p)
27: eval(quote(...), new.env())
26: eval(quote(...), new.env())
25: if (renv_bootstrap_load(project, libpath, version))
      return(TRUE) at activate.R#1159
24: renv::load(project) at activate.R#847
23: renv_load_finish(project, lockfile)
22: renv_load_report_synchronized(project, lockfile)
21: (function() {
        renv_scope_options(renv.verbose = FALSE)
        status(project = project, sources = FALSE)
    })()
20: status(project = project, sources = FALSE)
19: renv_status_impl(project, libpaths, lockpath, sources, cache)
18: renv_snapshot_dependencies(project, dev = FALSE)
17: dynamic(list(project = project, type = type, dev = dev), renv_snapshot_dependencies_impl(project, 
        type, dev))
16: the$dynamic_objects[[id]] %||% {
        dlog("dynamic", "memoizing dynamic value for '%s'", id)
        value
    }
15: renv_snapshot_dependencies_impl(project, type, dev)
14: withCallingHandlers(renv_dependencies_impl(path = path, root = project, 
        field = "Package", errors = config$dependency.errors(), dev = dev), 
        renv.dependencies.problems = function(cnd) {
            if (identical(config$dependency.errors(), "ignored")) 
                return()
            if (interactive() && !proceed()) 
                cancel()
        }, renv.dependencies.elapsed_time = function(cnd) {
            if (!type %in% c("packrat", "implicit")) 
                return()
            elapsed <- cnd$data
            limit <- getOption("renv.dependencies.elapsed_time_threshold", 
                default = 10L)
            if (elapsed < limit) 
                return()
            lines <- c("", "NOTE: Dependency discovery took %s during snapshot.", 
                "Consider using .renvignore to ignore files, or switching to explicit snapshots.", 
                "See `?renv::dependencies` for more information.", 
                "")
            writef(lines, renv_difftime_format(elapsed))
        })
13: renv_dependencies_impl(path = path, root = project, field = "Package", 
        errors = config$dependency.errors(), dev = dev)
12: renv_dependencies_discover(files, progress, errors)
11: bapply(paths, renv_dependencies_discover_impl)
10: lapply(x, f, ...)
 9: FUN(X[[i]], ...)
 8: tryCatch(filebacked("dependencies", path, callback), error = function(cnd) {
        warning(cnd)
        NULL
    })
 7: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: value[[3L]](cond)
 4: warning(cnd)
 3: withRestarts({
        .Internal(.signalCondition(cond, message, call))
        .Internal(.dfltWarn(message, call))
    }, muffleWarning = function() NULL)
 2: withOneRestart(expr, restarts[[1L]])
 1: doWithOneRestart(return(expr), restart)
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Platform: x86_64-pc-linux-gnu (64-bit)

[jabenninghoff]

@kevinushey, I have a reproducible example. I am seeing a similar error when restarting R after upgrading to renv 1.0.0:

Restarting R session...

- Project '~/GitHub/rtraining' loaded. [renv 1.0.0]
Warning messages:
1: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
2: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1
ℹ Loading rtraining

• The main branch of this project uses renv 0.17.3 and has no warning messages: https://github.com/jabenninghoff/rtraining
• The renv-update branch uses renv 1.0.0 and generates the warning message: https://github.com/jabenninghoff/rtraining/tree/renv-update
• The warnings occur when running renv/activate.R (removing this from .Rprofile eliminates the error).
• Adding the suggested settings (options(error = renv:::renv_error_handler_call()); options(warn = 2L)) changes the error message but doesn't provide additional detail:

Restarting R session...

- Project '~/GitHub/rtraining' loaded. [renv 1.0.0]
Error in is.na(value) : 
  (converted from warning) (converted from warning) is.na() applied to non-(list or vector) of type 'language'

Interestingly, I performed the upgrade from 0.17.3 to 1.0.0 using the commands:

renv::update("renv")
renv::snapshot()

However, when I try the following I get an error:

> renv::upgrade()
A new version of the renv package will be installed:

# CRAN ===============================
- renv   [0.17.3 -> 1.0.0]

This project will use the newly-installed version of renv.

Do you want to proceed? [y/N]: y
Installing renv [1.0.0] ...
	OK [linked cache in 0.76 milliseconds]
Warning messages:
1: In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1
2: In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1
warning messages from top-level task callback 'renv_sandbox_task'
Warning messages:
1: In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1
2: renv background task 'renv_sandbox_task' failed; it will be stopped 
warning messages from top-level task callback 'renv_snapshot_task'
Warning message:
In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1
Error in runHook(".onLoad", env, package.lib, package) : 
  lazy-load database '/Users/jabenninghoff/Library/Caches/org.R-project.R/R/renv/library/rtraining-be68765c/R-4.3/x86_64-apple-darwin20/renv/R/renv.rdb' is corrupt
In addition: Warning message:
In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1

I've upgraded several of my R packages to renv 1.0.0 with no issue; rtraining is the only one affected - the key difference could be the large number of dependencies in the project.

[JZschache]

Hi,

I had the same issue after upgrading to 1.0.0.

The following warnings occured whenever I called renv::status() or renv::init():

Warning messages:
1: In is.na(value) :
  is.na() applied to non-(list or vector) of type 'language'
2: In if (is.na(value)) default else as.logical(value) :
  the condition has length > 1

I tracked it down to an Rmd-file with the following chunk using a conditional evaluation:

```{r load_data, eval=!use_cache}
...

(The variable use_cache is defined in a previous chunk.)

I solved this by not using the negation:

```{r load_data, eval=not_use_cache}
...

The warnings disappeared afterwards.

Hope this helps others as well.

[hadley]

I think this is coming from truthy() when called inside renv_dependencies_discover_chunks_ignore().

Looks like the problem was caused in 314009b#diff-10360dfb4fa51b737341a4b5e8d5ea9758b1dcd3a9fb923349ee866120191a60 by removal of the is.call() block.

It's probably worth breaking up truthy() into two functions — one can be used for env vars (90% of the existing usage) and the other for parsing knitr options.