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.