Updating r

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Old packages: 'BBmisc', 'genefilter', 'Genomic Alignments', 'Genomic Ranges', 'IRanges', 'MASS', 'reshape2', 'Rgraphviz', 'RJSONIO', 'rtracklayer' Update all/some/none?

[a/s/n]: Bioc Installer::use Devel() Installing package into ‘/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1’ (as ‘lib’ is unspecified) trying URL ' Installer_1.15.5gz' Content type 'application/x-gzip' length 14144 bytes (13 Kb) opened URL ================================================== downloaded 13 Kb * installing *source* package ‘Bioc Installer’ ... Bioconductor version 3.0 (Bioc Installer 1.15.5), ?

It is important to be aware that R is an evolving software project, whose behaviour changes over time.

In general base R is very conservative about making changes that break backwards compatibility.

CPU resource allocated over time is another common OS variable that is worth monitoring.

updating r-55updating r-8updating r-29

Alongside R profiling functions such as profvis (see Section 7.2), system monitoring provides a useful tool for understanding how R is performing in relation to variables reporting the OS state, such as how much RAM is in use, which relates to the wider question of whether more is needed (covered in Chapter 3).

It explores how the operating system, R version, startup files and IDE can make your R work faster.

This chapter describes the set-up that will enable a productive workflow.

approaches to versioning, see the newsletter and version numbering developer reference.

Rarely, underlying changes in the operating system require ALL installed packages to be recompiled for source (C or Fortran) compatibility.

bioc Lite for help 'Bioc Installer' changed to version 1.15.5 bioc Valid() * session Info() R version 3.1.0 Patched (2014-05-06 r65533) Platform: x86_64-unknown-linux-gnu (64-bit) ... update with bioc Lite() * Packages too new for Bioconductor version '3.0' ...

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