Install Problems - BiocInstaller

[okiewhaler]

I'm eager to try this out - as per a recommendation from good colleague Eric Archer. Unfortunately, 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.

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)

Any help would be greatly appreciated.

All the best,

Matt

[DrK-Lo]

Hi Matt, Have you tried updating R? It looks like the version of R you are using is earlier than is required by the package. "ERROR: this R is version 3.3.1, package 'BiocInstaller' requires R >= 3.4.0"

[okiewhaler]

Hi Katie - Thanks for the response. This error occurs with the latest version of R for OS 10.9+ (as per CRAN), which is 3.3.1 http://cran.us.r-project.org/bin/macosx/

I see there is an devel version of R 3.4 available through the https://r.research.att.com/ ; as you can imagine, I'm hesitant to use this because of instability.

Does this mean that the newest version of BiocInstaller is not available for R 3.3.1 on Mac OS 10.9+? More importantly, is there a work-around for installing MINOTAUR on OS 10.9+ without BiocInstaller and R 3.4? Using an earlier version of BiocInstaller?

I have tried installing BioConduncter independently via the website before installing devtools (and after devtools), but to no avail. Changing the order of install still results in the same error https://www.bioconductor.org/install/

Any suggestions would be greatly appreciated. Thanks again for your time.

Matt

[hlapp]

It seems to be that the question about why there is a dependency on a development version of R is one for Bioconductor, not for the MINOTAUR package.

Perhaps the issue can be avoided by installing the Bioconductor package(s) in question prior to installing MINOTAUR through Github?

[okiewhaler]

Thanks Hilmar - I've tried your suggestion of installing BiocInstaller before MINOTAUR, but it is the newest version of BiocInstaller that is throwing the error. I'll channel my energy toward the BioConducter developers now as it does seem to be an issue with them, not with MINOTAUR (Although I am surprised no one else has had this issue). Thanks for your help!

[okiewhaler]

Hi All - I posted this to the BioConductor help site and they got back to me with a quick and easy work around. The dialogue is here; https://support.bioconductor.org/p/88794/

Includes this little nugget for you as the developers:

Actually looking more at this, the DESCRIPTION file of NESCent/MINOTAUR indicates that it will use

Remotes: github::Bioconductor-mirror/BiocInstaller,
github::Bioconductor-mirror/OmicCircos, github::rstudio/DT

implying that the author intends for the package to be using the devel (implicit @master github remote) branch of R and Bioconductor. Whether this is intentional or not is unclear, but should be taken up as a MINOTAUR issue. (devtools I think does the right thing with Bioconductor dependencies, without specifying a remote).

---

Hope this streamlines things - but it works now with the help of the link above. Thanks!!

[DrK-Lo]

@caitiecollins @bobverity I am also having this issue - can we fix the version of Bioconductor that is in the DESCRIPTION file of MINOTAUR?