genefilter XML problem

General
1

Whenever I try to load the genefilter package using

library(genefilter)

I get

Error: package or namespace load failed for ‘genefilter’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘XML’

What do I do?

2

Install the missing package

install.packages("XML")
3

I tried that, but it is giving me

Warning in install.packages :
  package ‘XML’ is not available (for R version 3.6.3)

I am new to R, so I am struggling with this.

4

The XML package requires R >= 4.0.0 so you need to update your R version to be able to install it. You are using a very old R version so it would be a good thing to do anyway.

5

I did that but then it gives me genefilter is not compatible for 4.0.2

6

Can you show the actual error message you get? You are not providing enough information to help you

7

Sorry here,

> install.packages("genefilter")
WARNING: Rtools is required to build R packages but no version of Rtools compatible with the currently running version of R was found. Note that the following incompatible version(s) of Rtools were found:

  - Rtools 3.5 (installed at C:\Users\anike\R-3.6.3\Rtools)

Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
  package ‘genefilter’ is not available (for R version 4.0.2)

and when I go to install Rtools

> install.packages("Rtools")
WARNING: Rtools is required to build R packages but no version of Rtools compatible with the currently running version of R was found. Note that the following incompatible version(s) of Rtools were found:

  - Rtools 3.5 (installed at C:\Users\anike\R-3.6.3\Rtools)

Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
  package ‘Rtools’ is not available (for R version 4.0.2)
8

I even tried the code I found on bioconductor's website (https://bioconductor.org/packages/release/bioc/html/genefilter.html)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("genefilter")

And it gives me

Error: Bioconductor version '3.10' requires R version '3.6'; see
  https://bioconductor.org/install
9

Rtools is not an R package, it is a separate software that you need to install in your system, for R 4.0.2 you need to install RTools40, you can download it from here
https://cran.r-project.org/bin/windows/Rtools/

10

Update your BiocManager version, for R 4.0.2 you have to use Bioconductor version '3.11'

install.packages("BiocManager")
11

I am currently downloading the Rtools40.

Also, is there a way to specify which bioconductor version I want to download because the install.package is installing the 3.10

12

Try running this command

update.packages(repos='https://cran.rstudio.com/', ask=FALSE, checkBuilt=TRUE)
13

Thank you so much.

I found that the following code updates the Bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.11")

It seems to have solved the problem.

14

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