Is Bioconductor 3.0 compatible with R 3.1.2?
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 2 days ago
United States

In the Bioconductor 3.0 announcement, I read

  •  "Bioconductor 3.0 is compatible with R 3.1.1".
  • "Install R 3.1.1. Bioconductor 3.0 has been designed expressly for this version of R"

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!

version compatibility • 4.1k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States

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

 

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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 locale

 R 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

 

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States

Yes, it will work. But consider upgrading to R-3.1.2 instead of doing biocLite("BiocUpgrade").

 

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@marco-blanchette-5439
Last seen 9.4 years ago
United States/Kansas City/Stowers Insti…

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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Entering edit mode

Remember that R is case-sensitive -- "BiocUpgrade"

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