Recently, I started learning differential gene expression analysis using Affymetrix microarrays with Rstudio. Then, my R console started showing this warning message:
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’I installed 'oligo' for this analysis, so probably that's why I didn't get this message before. This kept appearing whenever I started a new R session. Sometimes, when I installed a new package, it appeared in the middle of the installation process.
Eventually, this Github page's advice, update both R and Bioconductor release, cleared the warning.
Just FYI, my old versions were the following; R ( 4.0.2 ), Bioconductor ( 3.11 ).
Checking the Bioconductor's version
> library(BiocManager)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.11' is out-of-date;
the current release version '3.12' is available with R version '4.0';
see https://bioconductor.org/installChecked "https://bioconductor.org/install/" to know how to install a newer version and installed it:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.12")Checked the newly installed Bioconductor's version:
> BiocManager::version()
[1] '3.12'When I installed the newer Bioconductor, I had these warnings. But they were also cleared after I updated my R to 4.0.3.
Warning: package 'BiocStyle' was built under R version 4.0.3
Warning: package 'limma' was built under R version 4.0.3
Warning: package 'minfi's was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'Biostrings' was built under R version 4.0.3
Warning: package 'XVector' was built under R version 4.0.3
Warning: package 'bumphunter' was built under R version 4.0.3
Warning: package 'missMethyl' was built under R version 4.0.3
Warning: package 'Gviz' was built under R version 4.0.3
Warning: package 'DMRcate' was built under R version 4.0.3
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
Warning: replacing previous import 'rmarkdown::pdf_document' by 'BiocStyle::pdf_document' when loading 'methylationArrayAnalysis'
Warning: replacing previous import 'rmarkdown::html_document' by 'BiocStyle::html_document' when loading 'methylationArrayAnalysis'
Warning: replacing previous import 'rmarkdown::md_document' by 'BiocStyle::md_document' when loading 'methylationArrayAnalysis'
Updating R
I wanted to try 'updateR()' but as many people were struggling with this method, I couldn't find a solution for the password error.
So I gave up going this way, and instead, installed a new one from R CRAN: https://cran.r-project.org/bin/macosx/. (This page is for Mac. Linux & Windows users can find their versions from https://cran.r-project.org/ .)
To those who want to keep the installed packages, this stackoverflow might be helpful, though I didn't try it this time.
My "library" stays intact
Long story short, after installing the latest R, somehow my previously installed packages were intact, and I was able to call them from my new R. It might be because my update was within the same version (in my case from 4.0.2 to 4.0.3). This was unexpected (in a good way); I am so happy that I don't have to reinstall all my packages from scratch.
When I will update my version to 5.0.0 or older, maybe I will try the advice written in the above stackoverflow link.
# Before Updating R
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
......
...... # (continue)
# After the Update
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
......
...... # (continue)It seems all goes well now, no warning messages anymore. Hope this works for you, too.