SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
avoid cummeRbund "getGenes" automatically sorting geneIDs GuiFF Bioinformatics 1 07-07-2014 10:05 AM
samtools installation error "cannot find -lcurses" ihelbig Bioinformatics 5 02-01-2013 11:48 AM
CummeRbund csDendro error: "need finite ylim values" when replicates=TRUE mebbert Bioinformatics 4 07-18-2012 08:22 AM
"Global median" function in R/Bioconductor? shuang Bioinformatics 1 05-10-2012 06:27 PM
SOAPdenovo error "cant find kmer" guru1985 De novo discovery 0 03-07-2012 01:21 PM

Reply
 
Thread Tools
Old 04-26-2013, 05:19 AM   #1
jhsandgren
Junior Member
 
Location: Stockholm, Sweden

Join Date: Nov 2010
Posts: 2
Default could not find function "readCufflinks" cummeRbund

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"
jhsandgren is offline   Reply With Quote
Old 04-29-2013, 05:14 AM   #2
dGho
Member
 
Location: Rochester, NY

Join Date: Jan 2013
Posts: 43
Default

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 is offline   Reply With Quote
Old 04-30-2013, 07:32 AM   #3
dGho
Member
 
Location: Rochester, NY

Join Date: Jan 2013
Posts: 43
Default

yeah, its not the space. sorry.
dGho is offline   Reply With Quote
Old 05-01-2013, 03:09 AM   #4
jhsandgren
Junior Member
 
Location: Stockholm, Sweden

Join Date: Nov 2010
Posts: 2
Default

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.
jhsandgren is offline   Reply With Quote
Old 10-22-2013, 07:36 PM   #5
tokitky
Junior Member
 
Location: MA

Join Date: Oct 2013
Posts: 4
Default

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)
tokitky is offline   Reply With Quote
Old 12-19-2015, 01:00 PM   #6
avi.sri
Junior Member
 
Location: New York

Join Date: Jul 2015
Posts: 1
Default Try this

library(cummeRbund)
avi.sri is offline   Reply With Quote
Reply

Tags
cummerbund, rna seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO