error installing cummerbund in R studio

Question

[sangita_b]

Hi I have installed R (for Windows) and R studio (desktop version). I am trying to install cummerbund however the package won't install. I have tried a number of things based on forum posts but nothing has worked so far- can anyone offer any advice? Please see script for details:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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> source('http://www.bioconductor.org/biocLite.R')
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite('cummeRbund')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘cummeRbund’
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/cummeRbund_2.18.0.zip'
Content type 'application/zip' length 7699754 bytes (7.3 MB)
downloaded 7.3 MB

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\mszskb\AppData\Local\Temp\RtmpAbsKsF\downloaded_packages
Old packages: 'foreign', 'Matrix'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/foreign_0.8-68.zip'
Content type 'application/zip' length 308971 bytes (301 KB)
downloaded 301 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/Matrix_1.2-10.zip'
Content type 'application/zip' length 2839443 bytes (2.7 MB)
downloaded 2.7 MB

package ‘foreign’ successfully unpacked and MD5 sums checked
package ‘Matrix’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\mszskb\AppData\Local\Temp\RtmpAbsKsF\downloaded_packages
> library(cummeRbund)
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, cbind, colMeans, colnames,
    colSums, 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

Loading required package: RSQLite
Error: package or namespace load failed for ‘RSQLite’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘digest’
Error: package ‘RSQLite’ could not be loaded

Thanks Sangita

[cpad0112]

 **there is no package called ‘digest’

[PK]

https://cran.r-project.org/web/packages/digest/index.html

check this

[PK]

Cummerbund needs lot of dependencies so make sure with dependencies. Download source zip file and then extract.

[sangita_b]

Thank you, I have done this. How do I install digest to R?

[PK]

Follow the above mentioned link and download. Download Zip file and install through Rstudio (select the Zip file through the Rstudio)

[garimav89]

but how should I select the zip file and then install it. please help??

[cpad0112]

you don't need to do that i.e download source file etc. In R studio, type "setRepositories()" and press enter. Several repositories appear with following heading: --- Please select repositories for use in this session ---. Type : 1 2 3 4 5 6 7 and press enter. Then type in " install.packages("cummeRbund", dependencies=TRUE)" This should download all the dependency packages as well.

As for your question, how to install via source zip file in windows, follow this post on SO: https://stackoverflow.com/questions/7075709/install-binary-zipped-r-package-via-command-line

[lakhujanivijay]

What is the output of

library(RSQLite)

[sangita_b]

Thank you. I have tried this, the following error comes up Error: package or namespace load failed for ‘RSQLite’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘digest’

[cpad0112]

You still don't have digest package installed.

if you have downloaded "digest" package, run following command in linux terminal (assuming that you are using linux and current directory is where digest package is located) You still don't have digest package installed.

$ R CMD INSTALL <digest package>

If you are still in R console/R studio, type in

$ install.packages("digest")

This should install digest package.