I got a same "error message" as you did and the package was still installed. I don't think that's the issue at all. Try saying no when asked if you want to update your packages as below to see if it helps.
> BiocManager::install("DESeq2")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/DESeq2_1.22.2.zip'
Content type 'application/zip' length 2552721 bytes (2.4 MB)
downloaded 2.4 MB
package ‘DESeq2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\username\AppData\Local\Temp\Rtmp4kcGs3\downloaded_packages
installation path not writeable, unable to update packages: cluster, MASS, Matrix,
mgcv, nlme, rpart, survival
Update old packages: 'annotate', 'assertthat', 'backports', 'Biobase',
'BiocInstaller', 'BiocParallel', 'biomaRt', 'Biostrings', 'broom', 'bumphunter',
'Cairo', 'callr', 'caret', 'circlize', 'cli', 'clipr', 'colorspace',
'data.table', 'devtools', 'fs', 'genefilter', 'GenomeInfoDb',
'GenomeInfoDbData', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges',
'ggplot2', 'git2r', 'glue', 'gtable', 'HDF5Array', 'highr', 'httpuv', 'IRanges',
'lazyeval', 'limma', 'mclust', 'minfi', 'multtest', 'openssl', 'pkgbuild',
'plotly', 'polyclip', 'polynom', 'preprocessCore', 'purrr', 'Rcpp', 'readxl',
'recipes', 'RefManageR', 'remotes', 'rhdf5', 'Rhdf5lib', 'rJava', 'rlang',
'rmarkdown', 'Rsamtools', 'rstudioapi', 'rtracklayer', 'rvest', 'S4Vectors',
'shiny', 'siggenes', 'stringi', 'SummarizedExperiment', 'tibble', 'tinytex',
'urltools', 'usethis', 'xfun', 'XVector', 'zlibbioc', 'zoo'
Update all/some/none? [a/s/n]:
n
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter,
Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:BiocGenerics’:
dims
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply
>
Is there a reason this post is tagged with DESeq2?
yes, the package i'm trying to install is DESeq2
yes, the package i'm trying to install is DESeq2
Next time when asking question you should consider: 1. Put everything shown in the console into code blocks. Right now you have you "error message" out of the code block so it was hard to read. 2. Use the
reprexpackage to capture a reproducible example of your issue. Right now your first code block is not informative because we don't know what happened when you type those into your R session.We are all very busy and help you on a volunteering basis, so you will have better answers if you make it easier for us to understand you at a glance.