DESeq2 Install in Jupyter Notebook
0
0
Entering edit mode
13 months ago
Lolo • 0

I am having trouble installing the DESeq2 package within a Jupyter Notebook. I have tried installing using Conda using a Python kernel, and using BiocManager running an R kernel and both methods are not working.

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

BiocManager::install("DESeq2")


conda install bioconda::bioconductor-deseq2


**Error Code when trying using BiocManager code above:**

Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)

Installing package(s) 'DESeq2'

also installing the dependencies ‘zlibbioc’, ‘SparseArray’, ‘GenomeInfoDb’, ‘XVector’, ‘S4Arrays’, ‘DelayedArray’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Biobase’, ‘BiocParallel’, ‘locfit’, ‘RcppArmadillo’


Warning message in install.packages(...):
“installation of package ‘zlibbioc’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘IRanges’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘Biobase’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘BiocParallel’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘locfit’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘RcppArmadillo’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘GenomeInfoDb’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘XVector’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘S4Arrays’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘SparseArray’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘GenomicRanges’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘DelayedArray’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘SummarizedExperiment’ had non-zero exit status”
Warning message in install.packages(...):
“installation of package ‘DESeq2’ had non-zero exit status”
Updating HTML index of packages in '.Library'

Making 'packages.html' ...
 done

Old packages: 'boot', 'cpp11', 'curl', 'data.table', 'MASS', 'Matrix', 'nlme',
  'RcppEigen'

No error code is generated when installing using Conda, but when I run library it says no package installed.

deseq2 Jupyter • 613 views
ADD COMMENT

Login before adding your answer.

Traffic: 3412 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6