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

[Uwe Ligges]

On 22.04.2026 13:30, Peter Dalgaard wrote:
> Thanks for spotting this, Hervé.
> 
> You are probably right that this condition should be checked for in the code.
> 
> However, we are in code freeze and the direct cause of the issue is that the PACKAGES file in the binaries directory on CRAN is out of sync with it contents (AFAICS some Archived pakages had their binaries removed, but they remained listed in PACKAGES).
> 
> In normal operation, the source dir should have a superset of the binary dir and the PACKAGES file likewise and the problem shouldn't appear.


Peter,

there are separate PACKAGES files for the source repository and each of 
the binary repositories.
A PACKAGES file should always be consistent with the contents in the 
corresponding repository, of course. It must not contain entries for 
packages that are unavailable in that repo.
Technically, in order to avoid race conditions in the source repo, the 
entry in PACKAGES is even removed even before the package (or at least a 
link to it) is moved  away from the source repository.

For binary repositories: Binaries are not instantly removed from binary 
repositories if corresponding sources are moved to the archives. So you 
cannot expect that the source repo is always a superset of packages of a 
binary repo.

Best,
Uwe

> 
> - Peter D.
> 
>> On 22 Apr 2026, at 00.35, Hervé Pagès <hpages.on.github using gmail.com> 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
>> hpages.on.github using gmail.com
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac using r-project.org
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> 


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