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Better document purpose of BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS #165

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mtmorgan opened this issue May 6, 2023 · 0 comments
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Better document purpose of BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS #165

mtmorgan opened this issue May 6, 2023 · 0 comments

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@mtmorgan
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mtmorgan commented May 6, 2023

  • see Bioc-devel mailing list thread at https://stat.ethz.ch/pipermail/bioc-devel/2023-May/019678.html
  • Purpose is to enable off-line use of BiocManager, including enforcing appropriate version of bioconductor for version of R, not to circumvent version check
  • Relevant changes are to
    \env{BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS} is an environment
    variable or global \code{options()} which, when set to \code{FALSE}, avoids
    the R and \emph{Bioconductor} version checks that are done by querying
    an online configuration file. Setting
    \env{BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS} to \code{FALSE} can speed
    package loading when internet access is slow or non-existent, but
    may result in out-of-date information about the current release and
    development versions of \emph{Bioconductor}. Offline users should
    set the \env{BIOCONDUCTOR_CONFIG_FILE} environment variable or option
    to a \code{.yaml} file similar to \url{https://bioconductor.org/config.yaml}
    for full offline use and version validation.
    (man page) and
    ## Offline use
    (vignette)
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