[R-SIG-Mac] utils:::.available.both() breaks install.packages() on Mac sonoma-arm64

[Hervé Pagès]

Also

     rbind(av.src[src_pkgs, ], av.bin[bin_pkgs, ])

should be

     rbind(av.src[src_pkgs, , drop=FALSE], av.bin[bin_pkgs, , drop=FALSE])

or bad things will happen if src_pkgs or bin_pkgs have length 1.

H.


On 21/04/2026 15:35, Hervé Pagès wrote:
> With R 4.6 >= r89829  we're seeing this install.packages() error on 
> Mac sonoma-arm64 in various places:
>
>     Error in av.src[pkg.bin, "Version"] : subscript out of bounds
>
> This happens for example with install.packages("OSTA.data", 
> repos=BiocManager::repositories()).
>
> Also started to happen in this GitHub action a few days ago: 
> https://github.com/HyrienLab/igblastr/actions/runs/24495733061/job/71590105822
>
> The error occurs in the new utils:::.available.both() function 
> introduced at r89827 in trunk and r89829 in R-4-6-branch (file 
> src/library/utils/R/packages.R). It can simply be reproduced with:
>
> utils:::.available.both("https://cran.r-project.org")
>
>     # Error in av.src[pkg.bin, "Version"] : subscript out of bounds
>
> It seems that the function should be able to handle the situation 
> where some binary packages in the repo don't have a corresponding 
> source package. Something like this maybe:
>
> .available.both <- function(repos, method, ...) {
>     ## "both" gets complicated as we have to use available.packages twice
>     fields <- c(tools:::.get_standard_repository_db_fields(), "File", 
> "Built")
>     av.src <- available.packages(contriburl = contrib.url(repos, 
> "source"), method = method, fields = fields, ...)
>     av.bin <- available.packages(contriburl = contrib.url(repos, 
> "binary"), method = method, fields = fields, ...)
>     ## we keep things simple in that we use source unless there is the 
> same binary version
>     ## so that we can get at the Built field. This is more simple than 
> in install.packages
>     ## since we only care about determining whether a package is new, 
> but not which type is
>     ## preferred - install.packages will sort that out.
>     all_src_pkgs <- row.names(av.src)
>     all_bin_pkgs <- row.names(av.bin)
>     dual_pkgs <- intersect(all_src_pkgs, all_bin_pkgs)
>     src_ver <- av.src[dual_pkgs, "Version"]
>     bin_ver <- av.bin[dual_pkgs, "Version"]
>     use_bin <- as.numeric_version(bin_ver) >= as.numeric_version(src_ver)
>     ## If for some reason 'src_ver' or 'bin_ver' contain NAs, they 
> would propagate
>     ## to 'use_bin', but can this ever happen?
>     use_bin[is.na(use_bin)] <- TRUE
>     src_pkgs <- c(setdiff(all_src_pkgs, dual_pkgs), dual_pkgs[!use_bin])
>     bin_pkgs <- c(setdiff(all_bin_pkgs, dual_pkgs), dual_pkgs[use_bin])
>     ## Returned matrix has 1 row per package in 'union(all_src_pkgs, 
> all_bin_pkgs)'.
>     rbind(av.src[src_pkgs, ], av.bin[bin_pkgs, ])
> }
>
> Best,
>
> H.
>
-- 
Hervé Pagès

Bioconductor Core Team
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