I'm getting an install error I haven't been able to surmount. I'm running R Version 3.3.1 through RStudio Version 0.99.903 on Mac OS 10.10.5.
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Here is the code I'm running with the error:
>rm(list = ls())
>install.packages("devtools", dependencies=TRUE)
>library(devtools)
>install_github("NESCent/MINOTAUR", build_vignettes=TRUE)
Downloading GitHub repo NESCent/MINOTAUR@master
from URL https://api.github.com/repos/NESCent/MINOTAUR/zipball/master
Installing MINOTAUR
Downloading GitHub repo Bioconductor-mirror/BiocInstaller@master
from URL https://api.github.com/repos/Bioconductor-mirror/BiocInstaller/zipball/master
Installing BiocInstaller
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL \
'/private/var/folders/tb/x8ht0yyn0fnb9j301ynw377r0000gn/T/RtmpenL3Be/devtools5f1722a9343/Bioconductor-mirror-BiocInstaller-9965cc7' \
--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests
ERROR: this R is version 3.3.1, package 'BiocInstaller' requires R >= 3.4.0
Error: Command failed (1)
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I then tried all iterations of installing Bioconducter from the website (https://www.bioconductor.org/install/) before/after installing 'devtools' to try to ensure BiocInstaller was the correct version:
>source("https://bioconductor.org/biocLite.R")
>biocLite()
But it still seems like the version of BioInstaller is dependent on a version of R that hasn't been released yet - at least for Mac OS.
Any suggestions would be greatly appreciated,
Matt
Hi Martin,
I am having the same issue with the "TCGAworkflow" package getting the same error:
ERROR: this R is version 3.3.2, package 'TCGAWorkflow' requires R >= 3.4.0
Error: Command failed (1)
In addition: Warning message:
package ‘TCGAWorkflowData’ is not available (as a binary package for R version 3.3.2)
I have proceeded as you recommended but I am still getting the same message. Any idea? Thanks
IOM
I'm not really sure what you've done; the error message says that you should be using R-devel (aka, R version 3.4.0) to use the version of TCGAworkflow that you're trying to use. You haven't really given enough information for a full diagnosis, e.g., how you're trying to install TCGAworkflow and the output of your sessionInfo() (R command).
Maybe related ... I'm currently reviewing a package called TCGAWorkflow and the accompanying TCGAWorkflowData. They aren't approved yet so they aren't in the Bioconductor repos. Any installation of both packages would have to be (on your own) from the github repos.
Hi Valerie,
I tried to install those packages and got this error
> devtools::install_github("BioinformaticsFMRP/TCGAWorkflowData")
Downloading GitHub repo BioinformaticsFMRP/TCGAWorkflowData@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAWorkflowData/zipball/master
Installing TCGAWorkflowData
"C:/R/R-3.3.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/iooo/AppData/Local/Temp/RtmpUhn8Yc/devtools1b14454e9e5/BioinformaticsFMRP-TCGAWorkflowData-3f36003" --library="C:/R/R-3.3.2/library" \
--install-tests
ERROR: this R is version 3.3.2, package 'TCGAWorkflowData' requires R >= 3.4.0
I did what Martin suggested (
remove.packages("BiocInstaller")and then in a new session installing BiocInstaller viasource("https://bioconductor.org/biocLite.R"). Then install the github package using upgrade_dependencies=FALSE argument) but still get the same error.Re-installing BiocInstaller will not help. You need to be using R devel (version >=3.4.0) to use these packages. Your R is 3.3.2. If you do upgrade to R 3.4.0, you need to (manually) install the data package before the software package; because these packages are not in the Bioconductor repo the dependencies can't be managed by functions in BiocInstaller.
These packages are not ready for prime time and I would suggest talking with the author before trying to use them. The last time I checked the workflow took over 30 minutes to run and required gigabytes of disk space. Because these packages are not yet approved, any further installation problems you have should be taken up with the author.
Valerie
Hi Valerie,
Thanks for the explanation, I did not know that. Cheers
IOM