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.