Trying to Install BiocLite

[ath]

Hi,

I am a biologist (not a programmer so please consider this) and i want to use this pipepline: https://www.biostat.jhsph.edu/~kkammers/software/CVproteomics/R_guide.html

The problem is that I cannot install biocLite in my R.

See code bellow please

BiocManager::install('biocLite')
'getOption("repos")' replaces Bioconductor standard
repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1
(2022-06-23)
Installing package(s) 'biocLite'
Old packages: 'cli', 'crayon', 'foreign', 'ggforce',
'ggridges', 'ggtree', 'graphlayouts', 'igraph',
'jsonlite', 'mosaicCore', 'nnet', 'RcppArmadillo',
'RCurl', 'readr', 'rlang', 'tidytree', 'timeDate',
'tinytex', 'vctrs', 'vroom', 'XML'
Update all/some/none? [a/s/n]:
n
Warning message:
package ‘biocLite’ is not available for Bioconductor version '3.15'

A version of this package for your version of R might be available elsewhere,
see the ideas at

biocLite("limma")
Error in biocLite("limma") : could not find function "biocLite"
biocLite("qvalue")
Error in biocLite("qvalue") : could not find function "biocLite"

[AlexisW]

biocLite is not a thing anymore, it was used in the old versions of Bioconductor to install packages, now you can directly use BiocManager::install() as you did above.

For example:

BiocManager::install("limma")

You will notice it's actually the code that now appears on the Bioconductor page of the package.

Just for reference, the point of biocLite is that it was not a package from the repositories, see the bottom of this page for how to install it (if you're curious).