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')
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