If the user uses bioconductor for biology projects in R and their R library becomes corrupted you can do this command in the R prompt.

> BiocManager::valid()

At the end of this command it will present a very large R function you can call to fix the installation. Just copy and paste the section that looks like the section in red into the R intepreter and it will try and "fix" the installation.

​

> BiocManager::valid()

* sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

Matrix products: default

BLAS: /apps/R/3.5.1-gcc4/lib64/R/lib/libRblas.so

LAPACK: /apps/R/3.5.1-gcc4/lib64/R/lib/libRlapack.so

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):

[1] BiocManager _1.30.10 compiler_3.5.1 tools_3.5.1

Bioconductor version '3.8'

* 116 packages out-of-date

* 0 packages too new

create a valid installation with

BiocManager::install(c(

_"annotate", "AnnotationDbi", "assertthat", "backports", "baySeq", "BH",_

_"Biobase", "BiocGenerics", "BiocInstaller", "BiocParallel", "biomaRt",_

_"bit", "bit64", "blob", "Cairo", "checkmate", "cli", "colorspace",_

_"cowplot", "curl", "data.table", "DBI", "DEGseq", "DelayedArray",_

_"dendextend", "DESeq", "DESeq2", "devtools", "digest", "edgeR", "evaluate",_

_"fansi", "formatR", "gage", "GeneCycle", "genefilter", "geneplotter",_

_"GenomeInfoDb", "GenomeInfoDbData", "GenomicFeatures", "GenomicRanges",_

_"GGally", "ggplot2", "ggridges", "git2r", "glue", "GO.db", "gtable",_

_"highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httr",_

_"igraph", "IRanges", "irlba", "jsonlite", "KEGGREST", "knitr", "lambda.r",_

_"lazyeval", "limma", "locfit", "markdown", "matrixStats", "mime",_

_"mixOmics", "monocle", "mvtnorm", "openssl", "org.Hs.eg.db",_

_"org.Mm.eg.db", "OrganismDbi", "pathview", "pcaMethods", "pheatmap",_

_"phyloseq", "pillar", "pkgconfig", "plotly", "plyr", "prettyunits",_

_"qvalue", "R6", "Rcpp", "RcppArmadillo", "RcppProgress", "RCurl", "Rdpack",_

_"reshape2", "rlang", "ROC", "RSQLite", "rstudioapi", "Rtsne", "S4Vectors",_

_"scales", "sctransform", "seriation", "stringi", "stringr",_

_"SummarizedExperiment", "TCC", "tibble", "tidyverse",_

_"TxDb.Mmusculus.UCSC.mm10.knownGene", "urltools", "whisker", "withr",_

_"xtable", "XVector", "yaml", "zlibbioc"_

), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date​

Source: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html

NOTE:

If you get an error saying that the directory isn't writable for some packages you will need to email the admins at rcsg@utsa.edu and notify them they may need to run

update.packages(ask = FALSE)

on the base installation to update the base packages.