Installing Bioconductor packages [R for BE/BA]

posted by Helmut Homepage – Vienna, Austria, 2018-06-17 15:36  – Posting: # 18911
Views: 615

Dear all,

recently it took me ages to realize that a certain package is not available at CRAN but at Bioconductor. Example: Say you want to install package foo from Bioconductor. First I suggest to update the packages from CRAN by the usual method. Open the R-console and

update.packages(checkBuilt=TRUE, ask=FALSE)

It is possible that binaries are not the latest releases. Then you get e.g.,

  There are binary versions available but the source versions are later:
             binary source needs_compilation
compositions 1.40-1 1.40-2              TRUE
logspline    2.1.10 2.1.11              TRUE
MASS         7.3-49 7.3-50              TRUE
polspline    1.1.12 1.1.13              TRUE
progress      1.1.2  1.2.0             FALSE
recipes       0.1.2  0.1.3             FALSE
spatstat     1.55-1 1.56-0              TRUE
stringi       1.1.7  1.2.3              TRUE
survival     2.41-3 2.42-3              TRUE

Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘gpuR’

If asked for compilation make sure that you have the right tools and know what you are doing. Otherwise, keep the binaries. Next:

source("https://bioconductor.org/biocLite.R")
biocLite("foo")

At the end you eventually get a list of old packages (both from CRAN and Bioconductor) and

Update all/some/none? [a/s/n]:

No idea whether packages at Bioconductor are always at the same release level than ones at CRAN. I suggest to chicken out (answering n) unless you know what you are doing.

Cheers,
Helmut Schütz
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