could not find function "readCufflinks" cummeRbund

[jhsandgren]

Hi,
I have used cummeRbund a bit recently with Cuffdiff outputs from runs on Galaxy. It has worked ok but the last few days it does not. I have tried to install the package again but no success. Please see below for my problems, the function "readCufflilnks" does not work, anyone know why? Many thanks!

Cuffdiff v 0.0.5
R studio v 0.97.449
R 2.15.3

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'cummeRbund'
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu...s/contrib/2.15
trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/cummeRbund_2.0.0.zip'
Content type 'application/zip' length 2607618 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Johanna\AppData\Local\Temp\RtmpcTUck6\downloaded_packages
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu...s/contrib/2.15
Warning message:
installed directory not writable, cannot update packages 'cluster', 'foreign', 'KernSmooth',
'lattice', 'Matrix', 'nnet', 'rpart', 'survival'
> getwd()
[1] "C:/Users/Johanna/Documents"
> setwd("C:/Users/Johanna/Documents/R/at_rt")
> list.files()
[1] "CDS_FPKM_differential_expression_testing"
[2] "CDS_FPKM_tracking"
[3] "CDS_overloading_diffential_expression_testing"
[4] "gene_differential_expression_testing"
[5] "gene_FPKM_tracking"
[6] "promoters_differential_expression_testing"
[7] "splicing_differential_expression_testing"
[8] "transcript_differential_expression_testing"
[9] "transcript_FPKM_tracking"
[10] "TSS_groups_differential_expression_testing"
[11] "TSS_groups_FPKM_tracking"
> library(cummeRbund)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

xtabs

The following object(s) are masked from ‘package:base’:

anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect,
lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called ‘colorspace’
Error: package ‘ggplot2’ could not be loaded
> cuff= readCufflinks (dbFile = "output_database",
+ geneFPKM = "gene_FPKM_tracking",
+ geneDiff = "gene_differential_expression_testing",
+ isoformFPKM = "transcript_FPKM_tracking",
+ isoformDiff = "transcript_differential_expression_testing",
+ TSSFPKM = "TSS_groups_FPKM_tracking",
+ TSSDiff = "TSS_groups_differential_expression_testing",
+ CDSFPKM = "CDS_FPKM_tracking",
+ CDSExpDiff = "CDS_FPKM_differential_expression_testing",
+ CDSDiff = "CDS_overloading_diffential_expression_testing",
+ promoterFile = "promoters_differential_expression_testing",
+ splicingFile = "splicing_differential_expression_testing",
+ rebuild = T)
Error: could not find function "readCufflinks"

[dGho]

I have to warn you I am pretty new to R, but I was lucky that mine was workingbut could it be the space between readCufflinks and the parenthesis? readCufflinks(...)

can you try it without the space and see if it works?

[dGho]

yeah, its not the space. sorry.

[jhsandgren]

I guess the package is not intalled correctly for some reason, but I do not know why.. It has worked on the same computer until recently.

[tokitky]

Hi

I have a similar problem.

Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called ‘colorspace’
Error: package ‘ggplot2’ could not be loaded

Error: could not find function "readCufflinks"[/QUOTE]

This means that ‘ggplot2’ are not installed and cummeRbund needs ggplots
to work.

So you should install 'ggplot2' beforehand as follows.

>install.packages("ggplot2", dependencies=TRUE)

[avi.sri]

Try this

library(cummeRbund)