downloading GOSeq R package issues

[RockChalkJayhawk]

I have been trying to install goseq for RNA-Seq analysis, but can't figure out why I can't install it.

I have tried:

> install.packages("goseq")
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘goseq’ is not available

AND

>     source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
>     biocLite("goseq",dependencies=TRUE)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] "goseq"
Please wait...

also installing the dependencies ‘RCurl’, ‘XML’, ‘biomaRt’, ‘rtracklayer’, ‘GenomicFeatures’, ‘geneLenDataBase’

then it downloads for a long time until I get this message:

* DONE (vsn)
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/home/shart3/R-2.11.1/library/GenomicFeatures’
ERROR: dependencies ‘GenomicFeatures’ are not available for package ‘GenomicFeatures.Hsapiens.UCSC.hg18’
* removing ‘/home/shart3/R-2.11.1/library/GenomicFeatures.Hsapiens.UCSC.hg18’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘geneLenDataBase’
* removing ‘/home/shart3/R-2.11.1/library/geneLenDataBase’
ERROR: dependencies ‘geneLenDataBase’ are not available for package ‘goseq’
* removing ‘/home/shart3/R-2.11.1/library/goseq’
Error in setwd(startdir) : cannot change working directory
Error in setwd(startdir) : cannot change working directory
Execution halted

The downloaded packages are in
	‘/tmp/RtmpyALyTc/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'widgetTools' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'RCurl' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'XML' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'biomaRt' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'tkWidgets' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'rtracklayer' had non-zero exit status
7: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'GenomicFeatures' had non-zero exit status
8: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'GenomicFeatures.Hsapiens.UCSC.hg18' had non-zero exit status
9: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'geneLenDataBase' had non-zero exit status
10: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'goseq' had non-zero exit status

This seems like a pretty simple R issue, but I don't know much about it.

Any ideas?

[Jasmine]

Looks like some packages which goseq needs were not installed properly.

widgetTools seems to be the first package which failed to install. You can find the widgetTools from below site. You can download the package and install from Packages>Install package(s) from local zip file.

http://www.bioconductor.org/packages/2.3/bioc/html/widgetTools.html

Sometimes related packages are not installed properly and need to install manually.

I quickly tested to install goseq. I had no problem to install it. I tried on Windows Vista 64-bit version of R.

I'm not sure how much my information is helpful for you but I didn't know the goseq package, so thank you for the post.

Good luck!

Jasmine

[RockChalkJayhawk]

Looks like some packages which goseq needs were not installed properly.

widgetTools seems to be the first package which failed to install. You can find the widgetTools from below site. You can download the package and install from Packages>Install package(s) from local zip file.

http://www.bioconductor.org/packages/2.3/bioc/html/widgetTools.html

Sometimes related packages are not installed properly and need to install manually.

I quickly tested to install goseq. I had no problem to install it. I tried on Windows Vista 64-bit version of R.

I'm not sure how much my information is helpful for you but I didn't know the goseq package, so thank you for the post.

Good luck!

Jasmine

Thanks Jasmine. I was able to get it installed. Actually something was wrong with my RCurl, so I reinstalled R and it is installed and working.

Unfortunately now I ran into a problem in using the package. I have a file that looks like this

A1CF 	 1
A2LD1 	 0
A2M 	 0
A4GALT 	 1
AAA1 	 0
AAAS 	 0
AACS 	 0
AACSL 	 0
AADAC 	 0
AADAT 	 0

and I run using this:

library("goseq")
DvR<-read.delim("DMSOvRif.goseq",header=FALSE)
RifTest<-DvR[,-1]
pwf=nullp(RifTest,"hg19","geneSymbol")

which gives me the following error:

Loading hg19 length data...
Error in if (hi <= low) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In library() : library ‘/usr/lib/R/site-library’ contains no packages

Ideas?

[Jasmine]

Hi RockChalkJayhawk,

I think your data doesn't have id.

There is an example of nullp help,

data(prostate)
pwf <- nullp(genes, 'hg19', 'ensGene')

genes object has names,

names(genes)

This is is the gene ID formats available from the UCSC genome browser, according to the help.

?nullp

gives the help information. I think you can find more information there.

hope this helps. Good luck!

[Simon Anders]

Hi

[code]
> install.packages("goseq")

There are two main repositories of R packages, CRAN and Bioconductor. Do not use install.packages to install Bioconductor packages. Rather, use biocLite, as described here:

http://bioconductor.org/docs/install/

Simon

[RockChalkJayhawk]

Hi



There are two main repositories of R packages, CRAN and Bioconductor. Do not use install.packages to install Bioconductor packages. Rather, use biocLite, as described here:

http://bioconductor.org/docs/install/

Simon

Got it.

Thanks Simon.

[MDY]

We've already cleared this up in private correspondence, but I thought it was worth posting here in case anyone else runs into a similar problem.

The names being used for each gene contain a trailing space at the end. GOseq tries to match the gene names given to those in the database exactly and fails because of this trailing space. That is, "A2M "!="A2M". Removing the unwanted spaces from the name fixes the issue.