BiocManager::valid() not working within reprex::reprex()

[PeteHaitch]

Running from a new R session:

> BiocManager::valid()

* sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] repete_0.0.0.9011 devtools_1.13.5  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17           lobstr_0.0.0.9000     
 [3] XVector_0.21.2         magrittr_1.5          
 [5] GenomicRanges_1.33.6   BiocGenerics_0.27.0   
 [7] zlibbioc_1.27.0        IRanges_2.15.14       
 [9] munsell_0.5.0          colorspace_1.3-2      
[11] rlang_0.2.1            stringr_1.3.1         
[13] GenomeInfoDb_1.17.1    plyr_1.8.4            
[15] tools_3.5.0            parallel_3.5.0        
[17] withr_2.1.2            fortunes_1.5-4        
[19] yaml_2.1.19            digest_0.6.15         
[21] GenomeInfoDbData_1.1.0 BiocManager_1.29.45   
[23] pryr_0.1.4             S4Vectors_0.19.12     
[25] bitops_1.0-6           codetools_0.2-15      
[27] RCurl_1.95-4.10        memoise_1.1.0         
[29] stringi_1.2.3          compiler_3.5.0        
[31] scales_0.5.0           stats4_3.5.0          

Bioconductor version '3.8'

  * 0 packages out-of-date
  * 2 packages too new

create a valid installation with

  BiocManager::install(c(
    "hms", "reprex"
  ), update = TRUE, ask = FALSE)

Warning message:
0 packages out-of-date; 2 packages too new 

Running as reprex::reprex(x = BiocManager::valid()):

BiocManager::valid()
#> Error in repos[["CRAN"]]: subscript out of bounds

Created on 2018-06-13 by the reprex package (v0.2.0).

Any ideas? The combo of reprex::reprex() and BiocManager::valid() will be valuable when asking for minimal bug reports.

[LiNk-NY]

Hi Pete, @PeteHaitch
This seems like an issue with the options not being used in the package.
I'm not sure where in the reprex package these options get lost.

options("repos"); BiocManager::valid()
#> $repos
#> [1] "https://cloud.r-project.org" "https://cloud.r-project.org"
#> Error in repos[["CRAN"]]: subscript out of bounds
#> $repos
#> [1] "https://cloud.r-project.org" "https://cloud.r-project.org"

Created on 2018-07-06 by the reprex package (v0.2.0).

[PeteHaitch]

Are you saying you think it's a reprex issue rather than a BiocManager issue? If so, I'll report it there.

[LiNk-NY]

Hi Pete, @PeteHaitch
Basically, the package creates a clean environment from which the example code is run
(in order to ensure reproducibility).
This is more of a feature of the package although they should have a way of
setting options as part of the reprex. Perhaps there is a way but I'm not familiar with the package.
@jennybc can surely provide insights.

Regards,
Marcel

[jennybc]

To peel the onion a bit more, I wonder if this is a problem with callr? If I follow the above discussion, it is a problem that the return value for options("repos") is unnamed and therefore the attempt to get the "CRAN" element fails. Do I have that right?

reprex "just" prepares a .R file, marked up with some comments relevant to knitr, then calls rmarkdown::render() on it in a fresh R session, using callr::r() (see note).

I'm not sure why the name stripping happens but I can reproduce it with callr alone. FYI callr adds a CRAN repo (https://cloud.r-project.org), although the related code sure looks like it should return a named vector. I'm not sure how the names of "repos" are getting lost.

> getOption("repos")
                       CRAN 
"https://cran.rstudio.com/" 
attr(,"RStudio")
[1] TRUE
> callr::r(function() getOption("repos"))
[1] "https://cran.rstudio.com/"   "https://cloud.r-project.org"
> callr::r_safe(function() getOption("repos"))
[1] "https://cran.rstudio.com/"   "https://cloud.r-project.org"

Note: Technically, reprex::reprex() calls callr::r_safe() because that was necessary with a previous version of callr but the distinction isn't important in the current version.

[jennybc]

Hi @gaborcsardi do you have any insight?

[jennybc]

Maybe the names on repos are being lost here:

https://github.com/cran/callr/blob/d591dfee954a3a87cdf690c5e4953c4782ec17cb/R/check.R#L27

Small demo:

(x <- c(getOption("repos"), c(CRAN = "whatever")))
#>                       CRAN                       CRAN 
#> "https://cran.rstudio.org"                 "whatever" 
as.character(x)
#> [1] "https://cran.rstudio.org" "whatever"  

[gaborcsardi]

Indeed!

[LiNk-NY]

Yes, Jenny @jennybc that's right.
The code in BiocManager:::.repositories_base does repos[["CRAN"]] and since callr::r_safe strips the names, we get an error.

[jennybc]

This is now fixed in callr FWIW. Thanks for pointing it out.

[LiNk-NY]

Thanks Jenny!

[PeteHaitch]

Can confirm this has fixed the original issue. Thanks all!