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Question: error installing cummeRbund in R studio (Windows desktop)
0
gravatar for mszskb
5 months ago by
mszskb0
mszskb0 wrote:

Hi, 

I am trying to install cummeRbund using R studio. When loading the library the following error appears:

> library('cummeRbund')
Loading required package: rtracklayer
Error: package or namespace load failed for ‘rtracklayer’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘matrixStats’
Error: package ‘rtracklayer’ could not be loaded

Can anyone suggest how I can fix this?

 

Thanks

Sangita

The full script is below: 


> source("https://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\RtmpMHfxFZ\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
Loading required package: ggplot2
Find out what's changed in ggplot2 at
http://github.com/tidyverse/ggplot2/releases.
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘rtracklayer’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘matrixStats’
Error: package ‘rtracklayer’ could not be loaded
> "locate
+ libcurl"
[1] "locate\nlibcurl"
> "locate libcurl"
[1] "locate libcurl"
> save.image("E:\\install_cummerbund")
> sudo apt-get install libxml2 libcurl
Error: unexpected symbol in "sudo apt"
> options(install.packages.compile.from.source="never")
> library(BiocInstaller)
> 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\RtmpMHfxFZ\downloaded_packages
> library('cummeRbund')
Loading required package: rtracklayer
Error: package or namespace load failed for ‘rtracklayer’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘matrixStats’
Error: package ‘rtracklayer’ could not be loaded
> biocLite('cummeRbund')

ADD COMMENTlink modified 5 months ago • written 5 months ago by mszskb0
0
gravatar for Steve Lianoglou
5 months ago by
Genentech
Steve Lianoglou12k wrote:

It looks like you've somehow ended up with an incomplete installation because somehow somewhere someone is trying to load the matrixStats package, which doesn't appear to be installed.

Try installing that first, and try again.

install.packages("matrixStats")

 

ADD COMMENTlink written 5 months ago by Steve Lianoglou12k
0
gravatar for mszskb
5 months ago by
mszskb0
mszskb0 wrote:

Hi Steve, Thank you for your email. I tried your suggestion however the following error came (full script below)

> install.packages("matrixStats")
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning in install.packages :
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/matrixStats_0.52.2.zip'
Content type 'application/zip' length 1623476 bytes (1.5 MB)
downloaded 1.5 MB

package ‘matrixStats’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\mszskb\AppData\Local\Temp\RtmpkXwJpy\downloaded_packages


> biocLite('cummeRbund')
Error in biocLite("cummeRbund") : could not find function "biocLite"
> 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’
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES'
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\RtmpkXwJpy\downloaded_packages
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/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

ADD COMMENTlink written 5 months ago by mszskb0

Some comment as before, you are missing a required package "RSQLite". You need to carefully read through the "Error:" messages you are getting and sort those out.

It's not clear to me how this happened, but your installation seems quite broken for one reason or another. When you start from a "clean" R install and are careful to install your Bioconductor packages using biocLite, you typically shouldn't find yourself in the mess you seem to be in.

You might try blowing out your install and trying from scratch, or you can manually install the required packages as you go. You might try running BiocInstaller::biocValid() to see if it provides anything informative

 

ADD REPLYlink written 5 months ago by Steve Lianoglou12k
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