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[Bioc-devel] Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream

2 messages · Wolfgang Huber, Martin Morgan

Original
Wolfgang Huber
# 
Hi,

I get

 > BiocManager::install()
Error: Bioconductor version '3.13' requires R version '4.1'; R version is too new; see
  https://bioconductor.org/install

and this appears to be because of the last line in
Bioc    R  BiocStatus RSPM MRAN
?(29 lines omitted)?.
30 3.10  3.6 out-of-date <NA> <NA>
31 3.11  4.0 out-of-date <NA> <NA>
32 3.12  4.0     release <NA> <NA>
33 3.13  4.1       devel <NA> <NA>
34 3.13  4.2      future <NA> <NA>

Shouldn?t it say ?3.14? in the second element of the last line?
R Under development (unstable) (2021-05-04 r80261)
Platform: x86_64-apple-darwin20.4.0 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
BLAS:   /Users/whuber/R/lib/libRblas.dylib
LAPACK: /Users/whuber/R/lib/libRlapack.dylib

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

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

other attached packages:
[1] BiocManager_1.30.12 fortunes_1.5-4

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0

and I seem to have the most recent version of BiocManager as of today?s https://cran.r-project.org/web/packages/BiocManager/index.html 

??????

Btw the result of
[1] ?4.2.0?

is probably technically not correct, as it?s r-devel.

Kind regards
Wolfgang
Martin Morgan
# 
It's because Bioconductor won't be building (supporting) R-4.2 (R-devel) until six months from now, even in the 'devel' branch of Bioconductor. Bioc 3.14 (once it becomes available after the Bioconductor release) will use R 4.1 and the table will be updated to have line 34 as 3.14 / 4.1. There will be an entry 3.15/4.2/future, but there won't be a 3.15...

Martin

?On 5/4/21, 8:21 AM, "Bioc-devel on behalf of Wolfgang Huber" <bioc-devel-bounces at r-project.org on behalf of wolfgang.huber at embl.org> wrote:

    Hi,

    I get

     > BiocManager::install()
    Error: Bioconductor version '3.13' requires R version '4.1'; R version is too new; see
      https://bioconductor.org/install

    and this appears to be because of the last line in

    > BiocManager:::.version_map()
       Bioc    R  BiocStatus RSPM MRAN
    ?(29 lines omitted)?.
    30 3.10  3.6 out-of-date <NA> <NA>
    31 3.11  4.0 out-of-date <NA> <NA>
    32 3.12  4.0     release <NA> <NA>
    33 3.13  4.1       devel <NA> <NA>
    34 3.13  4.2      future <NA> <NA>

    Shouldn?t it say ?3.14? in the second element of the last line?


    > sessionInfo()
    R Under development (unstable) (2021-05-04 r80261)
    Platform: x86_64-apple-darwin20.4.0 (64-bit)
    Running under: macOS Big Sur 11.3

    Matrix products: default
    BLAS:   /Users/whuber/R/lib/libRblas.dylib
    LAPACK: /Users/whuber/R/lib/libRlapack.dylib

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

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

    other attached packages:
    [1] BiocManager_1.30.12 fortunes_1.5-4

    loaded via a namespace (and not attached):
    [1] compiler_4.2.0 tools_4.2.0

    and I seem to have the most recent version of BiocManager as of today?s https://cran.r-project.org/web/packages/BiocManager/index.html 

    ??????

    Btw the result of

    > BiocManager:::.get_R_version()
    [1] ?4.2.0?

    is probably technically not correct, as it?s r-devel.

    Kind regards
    Wolfgang

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