Question: Unable to install packages
0
gravatar for efratsh
7 days ago by
efratsh0
efratsh0 wrote:

Hello, after restarting the R studio, I'm unable to install packages, I keep getting the error: installation path not writeable, unable to update packages: class, cluster, codetools, MASS, Matrix, mgcv, nlme, rpart, survival I tried to:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
pkgs <- rownames(installed.packages())
BiocManager::install(pkgs, type = "source")

also to re-install R and Rstudio

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255    LC_MONETARY=Hebrew_Israel.1255
[4] LC_NUMERIC=C                   LC_TIME=Hebrew_Israel.1255    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.2     tools_3.5.2        yaml_2.2.0        

Can you please help? Thanks, Efrat

deseq2 software error • 103 views
ADD COMMENTlink modified 6 days ago by Anh N Tran0 • written 7 days ago by efratsh0

Is there a reason this post is tagged with DESeq2?

ADD REPLYlink written 7 days ago by Michael Love23k

yes, the package i'm trying to install is DESeq2

ADD REPLYlink written 7 days ago by efratsh0

yes, the package i'm trying to install is DESeq2

ADD REPLYlink written 7 days ago by efratsh0

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 reprex package 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.

ADD REPLYlink written 6 days ago by Anh N Tran0
Answer: Unable to install packages
0
gravatar for James W. MacDonald
7 days ago by
United States
James W. MacDonald49k wrote:

This isn't a Bioconductor question! None of the packages you mention are part of Bioconductor. In future you should ask questions about basic R stuff on r-help@r-project.org

That said, the packages you mention are all in the set of recommended packages, and if you installed R as a privileged user then they are usually then installed in a directory path that a user with less privileges cannot install to. So you should have got an error saying something about not having permissions to install. Edit

The message should look like this:

installation path not writeable, unable to update packages: class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, survival

Which is pretty clear, and if you had simply googled that message you would get 525 results, all of which pretty much say the same thing.

Which brings me to another point - if you did get an error saying something like that, and neglected to say anything about it, you are not helping yourself, or anybody else. What you did is only half of the story, and any errors or warnings returned by R when you did it is the other half. What you have told us is similar to taking your car to the mechanic and saying 'it doesn't work', which could mean any number of things, and without specifically describing what happened and the errors/warnings you are expecting people to guess, which is usually met with no response or an unhelpful one.

ADD COMMENTlink modified 7 days ago • written 7 days ago by James W. MacDonald49k

all this packages worked before, only bioconductor pakages are not working, other do.

ADD REPLYlink written 7 days ago by efratsh0

Again, that doesn't help. Your original complaint was that you couldn't install recommended packages, with no mention about DESeq2. Now you say something cryptic about some packages working and others not working. Put yourself in our shoes. How could anybody read what you have said and use that to help you?

What does 'only bioconductor packages are not working' mean, exactly? You need to copy and paste the output from running BiocManager::install, showing the errors you are getting, as well as the output from sessionInfo to show what version of Bioconductor you are using.

ADD REPLYlink written 7 days ago by James W. MacDonald49k

the exact command is BiocManager::install("DESeq2", version = "3.8") I tried other packages like: BiocManager::install("GenomicFeatures", version = "3.8") BiocManager::install("Rsamtools", version = "3.8") they all failed with the same message. I did provide sessionInfo() on the original message

ADD REPLYlink written 6 days ago by efratsh0

They all failed with what message?

ADD REPLYlink written 6 days ago by James W. MacDonald49k

I think he referred to the error message:

installation path not writeable, unable to update packages: class, cluster, codetools, MASS, Matrix, mgcv, nlme, rpart, survival

He mentioned that in the first sentence of his question, but did not put it as a code block.

ADD REPLYlink written 6 days ago by Anh N Tran0
Answer: Unable to install packages
0
gravatar for Anh N Tran
6 days ago by
Anh N Tran0
Anh N Tran0 wrote:

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
>
ADD COMMENTlink modified 6 days ago • written 6 days ago by Anh N Tran0
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