Question

goseq Error: could not find function "supportedOrganisms"

0

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colaneri ▴ 30

@colaneri-7770

Last seen 5.0 years ago

United States

I installed goseq and when I call:

SO <- supportedOrganisms()
Error: could not find function "supportedOrganisms"
supportedGenomes()
Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : 
  subscript out of bounds

A Similar question have been posted here:

GoSeq SupportedGenomes error

but following those suggestion did not help.

In the goseq Bioconductor site said that the goseq version is 1.26. However when I install it in my mac running R vesrion 3.2.2 I got the version 1.22. All my bioconductor packages have been updated to the last version. I do not understand why I did not get that function with my goseq package. Any different suggestion to fix this problem?

goseq • 1.7k views

ADD COMMENT • link updated 7.1 years ago by edmund.wright • 0 • written 7.1 years ago by colaneri ▴ 30

score 0 · Answer 1 · 2017-03-06

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 4 hours ago

United States

Yes. Update to the current version of R. R-3.2.2 is out of date by almost three years. You should be running R-3.3.3.

ADD COMMENT • link 7.1 years ago James W. MacDonald 65k

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James, sorry but I do not follow why updating to the current version of R will help. The package I am having problem with is older than this R 3.3.3 version and it should be working fine with my R version 3.2.2.

I check for the version you suggested at it looks is really new

News

R version 3.3.3 (Another Canoe) has been released on Monday 2017-03-06.

ADD REPLY • link 7.1 years ago colaneri ▴ 30

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Every six months we release a new version of Bioconductor that is tied to the current version of R. If you are using a version of R from 2015, then by definition you are also using Bioconductor packages from two years ago as well. You always want to be using the most current version of R and Bioconductor for a lot of reasons, not least of all because we don't support any older versions.

What that means is that when a bug is introduced (and in this situation the 'bug' was a change at the UCSC website that broke code in the rtracklayer package), we only update the current release and devel versions of the affected packages. So unless you are using the most current versions of R and Bioconductor, these bug fixes are unavailable to you because we don't fix old packages from two years ago - we just fix the current version.

ADD REPLY • link 7.1 years ago James W. MacDonald 65k

score 0 · Answer 2 · 2017-03-07

The function supportedOrganisms() wasn't added to the goseq package until March 2016, and it didn't become part of the official Bioconductor release until May 2016 (goseq 1.24.0).

You are running a version of the software that is older, so obviously you won't be able to use that function, or any other newer features of the package.

As James has explained to you, you can only install the latest version of goseq if you also install the latest version of R.

score 0 · Answer 3 · 2017-03-28

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edmund.wright • 0

@edmundwright-9173

Last seen 7.1 years ago

United Kingdom

I have updated my R to 3.3.3 version a week or so ago, and now find that "GOseq" package is not available for it. When I type:

install.packages("GOseq")

I get this:

Warning message:
package ‘GOseq’ is not available (for R version 3.3.3)

Is there a solution to this?

Many thanks,

Hugh Wright

ADD COMMENT • link 7.1 years ago edmund.wright • 0

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install.packages() does not look in the Bioconductor repository by default. Use Bioconductor's install function and capitalize the package name properly:

source("https://bioconductor.org/biocLite.R")
biocLite("goseq")

ADD REPLY • link 7.1 years ago Jenny Drnevich ★ 2.0k