Failed to parse 'renv.lock'

[KKamel67]

I tried to use the version 1.1.1 version of the renv package. After executing the renv::snapshot() command, when I open the project I get the following message :

Error in (function (err) : Failed to parse 'renv.lock':
input string 1 is invalid UTF-8

Traceback (most recent calls last):
20: source("renv/activate.R")
19: withVisible(eval(ei, envir))
18: eval(ei, envir)
17: eval(ei, envir)
16: local(...) at activate.R#2
15: eval.parent(substitute(eval(quote(expr), envir)))
14: eval(expr, p)
13: eval(expr, p)
12: eval(quote(...), new.env())
11: eval(quote(...), new.env())
10: renv_bootstrap_exec(project, libpath, version) at activate.R#1309
 9: if (!renv_bootstrap_load(project, libpath, version))
      renv_bootstrap_run(project, libpath, version) at activate.R#1139
 8: renv::load(project) at activate.R#994
 7: renv_lockfile_load(project)
 6: renv_lockfile_read(path)
 5: withCallingHandlers(json <- renv_json_read(text = contents), 
        error = function(err) {
            stop("Failed to parse 'renv.lock':\n", conditionMessage(err))
        })
 4: renv_json_read(text = contents)
 3: stop(json)
 2: <condition-handler>(...)
 1: stop("Failed to parse 'renv.lock':\n", conditionMessage(err))

Here are the session information :

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0    renv_1.1.1 

In the attached file, you can find the content of the renv.lock file.

renv_lock.txt

[jkylearmstrong]

This looks similar to an issue I have been having #2089 .

[kevinushey]

This issue should now be fixed in the development version of renv. To test, can you please try running:

renv::install("rstudio/renv")

then, restart R and see if you're now able to call renv::snapshot() without issue?

[KKamel67]

Thank you for your development. I just tried with the new renv version. The error message disappeared. But the project is slow for opening (more than 2min).

[kevinushey]

Can you try placing the following in your project's .Rprofile?

library(utils)
Rprof("startup.Rprof")
source("renv/activate.R")
Rprof(NULL)
summaryRprof("startup.Rprof")

Then, restart your R session. You should see a print-out of what functions were executed, and what took the most time. Can you share that?

[KKamel67]

Here are the outputs of the Rprof part

by_self.txt
by_total.txt

.

[kevinushey]

Thanks -- it looks like BiocManager is the culprit. Unfortunately it wants to make a web request just to determine if the current version of R is compatible with the version of Bioconductor being used...

I'll see if I can work around this.

[kevinushey]

I've just pushed a potential fix for this issue -- can you try once more installing the development version of renv and let me know if the issue persists?

renv::install("rstudio/renv")

[KKamel67]

Thanks -- it looks like BiocManager is the culprit. Unfortunately it wants to make a web request just to determine if the current version of R is compatible with the version of Bioconductor being used...

I'll see if I can work around this.

I thought it was fixed in a previous version without updating renv/activate.R.

[KKamel67]

Yes it looks ok for me.

No error message anymore to parse renv.lock.
Project opens fast.

[kevinushey]

Great, thanks for confirming. I'll try to get an update to CRAN early next week.