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Question: Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
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gravatar for harry.horsnell.17
5 weeks ago by
harry.horsnell.170 wrote:

Hi Everyone,

New user and first time posting to Bioconductor support page. I am also fairly new to R software

Come up with a slight issue loading the 'rnaseqGene' package from this workflow

http://www.bioconductor.org/help/workflows/rnaseqGene/#abstract

I am currently running the latest R version 3.4.4 for mac, however the 'rnaseqGene' package only seems to be compatible for 3.4.2

So my two questions are;

1) Is it possible for me to find a way to run 'rnaseqGene' package on my current R version 3.4.4

2) If not, what is the easiest way to get a 3.4.2 version for mac

Hope you can help and looking forward to interacting with the community

Thanks,

Harry

ADD COMMENTlink modified 5 weeks ago by shepherl ♦♦ 590 • written 5 weeks ago by harry.horsnell.170

Can you please post the commands and the ERROR you are seeing when you try to install the package. 

ADD REPLYlink written 5 weeks ago by shepherl ♦♦ 590

I tried on Windows and Linux and get the same result as the OP:

> library(BiocInstaller)
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("rnaseqGene")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) 'rnaseqGene'
installation path not writeable, unable to update packages: cluster, MASS,
  Matrix, mgcv, nlme, rpart, survival
Old packages: 'bindrcpp', 'curl', 'GenomicAlignments', 'RSQLite', 'viridis',
  'XML'
Update all/some/none? [a/s/n]: n
Warning message:
package 'rnaseqGene' is not available (for R version 3.4.3) 
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3   
> 
ADD REPLYlink written 5 weeks ago by James W. MacDonald46k

Of course, this is what appears in my console when using the command lines that is suggested on the workflow page linked in my original comment

 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite('rnaseqGene')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘rnaseqGene’
Warning message:
package ‘rnaseqGene’ is not available (for R version 3.4.4) 

ADD REPLYlink written 5 weeks ago by harry.horsnell.170
2
gravatar for shepherl
5 weeks ago by
shepherl ♦♦ 590
shepherl ♦♦ 590 wrote:

We just implemented the workflow download with biocLite() and works for Bioc 3.7 -

Could you try the old installation and see if this works; perhaps it should have only been advertised for the devel until the release:

source("http://bioconductor.org/workflows.R")

workflowInstall("rnaseqGene")
ADD COMMENTlink written 5 weeks ago by shepherl ♦♦ 590

Your suggestion has allowed me to load the "rnaseqGene" package into R version 3.4.4! Thanks for your help!

H

ADD REPLYlink written 5 weeks ago by harry.horsnell.170
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