Question

Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package

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harry.horsnell.17 • 0

@harryhorsnell17-15582

Last seen 6.5 years ago

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

rnaseq rnaseqgene R 3.4.2 Mac • 1.9k views

ADD COMMENT • link updated 6.6 years ago by shepherl 4.1k • written 6.6 years ago by harry.horsnell.17 • 0

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

ADD REPLY • link 6.6 years ago shepherl 4.1k

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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 REPLY • link 6.6 years ago James W. MacDonald 67k

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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 REPLY • link 6.6 years ago harry.horsnell.17 • 0

score 2 · Accepted Answer · 2018-04-17

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shepherl 4.1k

@lshep

Last seen 1 hour ago

United States

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 COMMENT • link 6.6 years ago shepherl 4.1k

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

H

ADD REPLY • link 6.6 years ago harry.horsnell.17 • 0