Installation of PCSF fails

moldach commented 4 years ago

I'm having trouble trying to install PCSF according to the instructions:

source("http://bioconductor.org/biocLite.R")
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
biocLite("topGO")
Error in biocLite("topGO") : could not find function "biocLite"

install.packages("devtools", dependencies=TRUE)
devtools::install_github("IOR-Bioinformatics/PCSF", repos=BiocInstaller::biocinstallRepos(),
                         dependencies=TRUE, type="source", force=TRUE)
Downloading GitHub repo IOR-Bioinformatics/PCSF@master
Error: Failed to install 'PCSF' from GitHub:
  there is no package called ‘BiocInstaller’

The installation should occur through BiocManager instead of biocLite as it's deprecated.

david-dd-amar commented 3 years ago

The following worked for me:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
devtools::install_github("IOR-Bioinformatics/PCSF", repos=BiocManager::repositories(),
                         dependencies=TRUE, type="source", force=TRUE)

Athishm0 commented 5 months ago

documentation PCHS.txt

Hi this is my first time making instructions on installing packages. The lab I am going to be doing my Honours project with had issues with installing the package. After some effort and multiple errors I installed it and recorded the steps I in this txt file.

for the last part of the installation, https://bioconductor.org/biocLite.R does not exit so you must...

download and install biocinstaller through https://bioconductor.org/packages//2.13/bioc/html/BiocInstaller.html, once downloaded, install through cmd bellow.

Rcmd: >install.packages("C:/Users/athis/Downloads/BiocInstaller_1.12.1.tar.gz", repos = NULL, type = "source")

library(BiocInstaller)

then:

Rcmd: >devtools::install_github("IOR-Bioinformatics/PCSF", repos=BiocInstaller::biocinstallRepos(), dependencies=TRUE, type="source", force=TRUE)

install(PCSF,C:/Users/athis/AppData/Local/R/win-library/4.4/00LOCK-PCSF/00new/PCSF/libs/x64) library(PCSF)

IOR-Bioinformatics / PCSF

Installation of PCSF fails #8

then: