In the Bioconductor 3.0 announcement, I read
Perhaps the above is the answer to my question, but I have to ask anyway...
Is it also compatible with 3.1.2? And, is there somewhere (else) that answers this question (more explicitly) on the BioC website?
Thanks!
Yes.
R-3.1.2 did not exist when the release announcement was written.
Bioconductor 3.0 is compatible with R-3.1.1, 3.1.2, and any future version of R-3.1.x.
Now that 3.1.2 has been released, maybe we'll update the versions of the release announcement on this site and on the Bioconductor site to say 3.1.x instead of 3.1.1.
Incidentally, the Windows and Linux build machines (for release) have been updated to 3.1.2 and tomorrow's builds will reflect this. The Mac machines have not yet been updated as CRAN has not yet made a binary available for Mac.
Dan
Yes, it will work. But consider upgrading to R-3.1.2 instead of doing biocLite("BiocUpgrade").
Finding that on my Mac running R 3.1.1, BioConductor installs version 2.14 only, take a look:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
> biocLite("biocUpgrade")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version
3.1.1.
Installing package(s) 'biocUpgrade'
Old packages: 'BatchJobs', 'BBmisc', 'RcppArmadillo'
Update all/some/none? [a/s/n]: a
trying URL 'http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.1/BatchJobs_1.5.tgz'
Content type 'application/x-gzip' length 401327 bytes (391 Kb)
opened URL
==================================================
downloaded 391 Kb
trying URL 'http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.1/BBmisc_1.8.tgz'
Content type 'application/x-gzip' length 267973 bytes (261 Kb)
opened URL
==================================================
downloaded 261 Kb
trying URL 'http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.1/RcppArmadillo_0.4.500.0.tgz'
Content type 'application/x-gzip' length 1212355 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb
The downloaded binary packages are in
/var/folders/wn/fg2m7tld0n560v1lzyhlx8b1knsw_h/T//RtmpqKCH0s/downloaded_packages
Warning message:
package ‘biocUpgrade’ is not available (for R version 3.1.1)
Does that make sense?
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version 2.3.6
Thanks, Dan, but, what about R 3.1.0?
Is BioConductor 3.0 compatible with R 3.1.0?
If not, then, why am I learning that " A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help" in the below? And what will happen if I do run BiocUpgrade in R 3.1.0 with Bioc 2.14, as suggested?
R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English localeR is a collaborative project with many contributors.Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)>
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
!> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en\
_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:[1] stats graphics grDevices datasets utils methods base
other attached packages:[1] BiocInstaller_1.14.3
loaded via a namespace (and not attached):[1] compiler_3.1.0 tools_3.1.0