AnswerBun.com

can I download DESeq2 in R 3.6.3 in Linux MInt?

Bioinformatics Asked on December 30, 2021

I am trying to download DESeq2 in R 3.6.3. Is it possible?
This is printed when I am trying: Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.6.3)
Thank you!

2 Answers

these errors are generated when I am doing what PPK suggested: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29) Installation path not writeable, unable to update packages: nlme, spatial, survival

BiocManager::install("DESeq2") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29) Installing package(s) 'DESeq2' Warning: dependency ‘XML’ is not available also installing the dependencies ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz' Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz' Content type 'application/x-gzip' length 1421076 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz' Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz' Content type 'application/x-gzip' length 2060061 bytes (2.0 MB)

downloaded 2.0 MB

ERROR: dependency ‘XML’ is not available for package ‘annotate’

  • removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
  • removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
  • removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’ ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
  • removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’

The downloaded source packages are in ‘/tmp/RtmphLXrZb/downloaded_packages’ Installation path not writeable, unable to update packages: nlme, spatial, survival Warning messages: 1: In install.packages(...) : installation of package ‘annotate’ had non-zero exit status 2: In install.packages(...) : installation of package ‘genefilter’ had non-zero exit status 3: In install.packages(...) : installation of package ‘geneplotter’ had non-zero exit status 4: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status

I have tried to instal XML and the other dependencies without success..

Answered by marilu on December 30, 2021

Bioconductor is a package management tool for R that allows you to install the appropriate package versions for your R version.

For R 3.6.3 you'll need Bioconductor 3.10:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.10")

Then you install DESeq2:

BiocManager::install("DESeq2")

Answered by PPK on December 30, 2021

Add your own answers!

Related Questions

Genewise: Failed to call blastwise.pl

0  Asked on January 28, 2021 by yp-chen

 

ATAC seq : Plotting insert sizes

1  Asked on January 26, 2021

 

Find CRISPR PAM-sites with python

1  Asked on January 21, 2021 by heibai

     

Microarray Meta-Analysis and Cross-Platform

1  Asked on January 20, 2021 by morteza-hadizadeh

 

Ask a Question

Get help from others!

© 2023 AnswerBun.com. All rights reserved. Sites we Love: PCI Database, MenuIva, UKBizDB, Menu Kuliner, Sharing RPP, SolveDir