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morota edited this page Dec 19, 2012
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chooseCRANmirror()summary(packageStatus()).packages(all = TRUE)
library()
installed.packages()setRepositories()# if that fails, then traceback() will tell you where the failure happened
install.packages("MyPackage.tar.gz", repos=NULL, type="source")find("vignette")
[1] "package:utils"
# see which package of "t" is the first on the search path
find("t")
[1] "package:Matrix" "package:base"search()
[1] ".GlobalEnv" "package:MCMCglmm" "package:corpcor"
[4] "package:ape" "package:coda" "package:Matrix"
[7] "package:tensorA" "package:lattice" "package:stats"
[10] "package:graphics" "package:grDevices" "package:utils"
[13] "package:datasets" "package:methods" "Autoloads"
[16] "package:base"
(.packages)
loadedNamespaces()
[1] "base" "fortunes" "graphics" "grDevices" "methods" "stats"
[7] "utils"
searchpaths()
[1] ".GlobalEnv"
[2] "/home/gota/R/i686-pc-linux-gnu-library/2.10/MCMCglmm"
[3] "/home/gota/R/i686-pc-linux-gnu-library/2.10/corpcor"
[4] "/home/gota/R/i686-pc-linux-gnu-library/2.10/ape"
[5] "/home/gota/R/i686-pc-linux-gnu-library/2.10/coda"
[6] "/usr/lib/R/library/Matrix"
[7] "/home/gota/R/i686-pc-linux-gnu-library/2.10/tensorA"
[8] "/usr/lib/R/library/lattice"
[9] "/usr/lib/R/library/stats"
[10] "/usr/lib/R/library/graphics"
[11] "/usr/lib/R/library/grDevices"
[12] "/usr/lib/R/library/utils"
[13] "/usr/lib/R/library/datasets"
[14] "/usr/lib/R/library/methods"
[15] "Autoloads"
[16] "/usr/lib/R/library/base"packageStatus()
Number of installed packages:
ok upgrade unavailable
/usr/local/lib/R/site-library 180 7 29
/usr/lib/R/site-library 0 0 0
/usr/lib/R/library 24 4 0
Number of available packages (each package counted only once):
installed not installed
http://cran.r-project.org/src/contrib 201 2731
update.packages(checkBuilt=TRUE) # or upgrade(packageStatus())
packageStatus()
Number of installed packages:
ok upgrade unavailable
/usr/local/lib/R/site-library 187 0 29
/usr/lib/R/site-library 0 0 0
/usr/lib/R/library 28 0 0
Number of available packages (each package counted only once):
installed not installed
http://cran.r-project.org/src/contrib 201 2731
# unavailable ones are all Bioconductor packages
# code from R-adimin
inst <- packageStatus()$inst
with(inst, inst[Status != "ok", c(1, 3, 13)])
Package Version Status
affy affy 1.28.0 unavailable
affydata affydata 1.11.10 unavailable
affyio affyio 1.18.0 unavailable
affyPLM affyPLM 1.26.1 unavailable
affyQCReport affyQCReport 1.28.1 unavailable
anchors anchors 3.0-4 unavailable
annaffy annaffy 1.22.0 unavailable
annotate annotate 1.28.1 unavailable
AnnotationDbi AnnotationDbi 1.12.0 unavailable
Biobase Biobase 2.10.0 unavailable
Biostrings Biostrings 2.18.4 unavailable
DynDoc DynDoc 1.28.0 unavailable
gcrma gcrma 2.22.0 unavailable
genefilter genefilter 1.32.0 unavailable
geneplotter geneplotter 1.28.0 unavailable
GenomicRanges GenomicRanges 1.2.3 unavailable
GO.db GO.db 2.4.5 unavailable
hgu95av2.db hgu95av2.db 2.4.5 unavailable
IRanges IRanges 1.8.9 unavailable
KEGG.db KEGG.db 2.4.5 unavailable
limma limma 3.6.9 unavailable
marray marray 1.28.0 unavailable
mogene10stv1cdf mogene10stv1cdf 2.7.0 unavailable
NTW NTW 1.0.0 unavailable
org.Hs.eg.db org.Hs.eg.db 2.4.6 unavailable
preprocessCore preprocessCore 1.12.0 unavailable
Rgraphviz Rgraphviz 1.28.0 unavailable
simpleaffy simpleaffy 2.26.1 unavailable
vsn vsn 3.18.0 unavailablepackageDescription("tools")
a <-installed.packages()
length(a)
[1] 2509
colnames(a)
[1] "Package" "LibPath" "Version" "Priority" "Depends" "Imports"
[7] "LinkingTo" "Suggests" "Enhances" "OS_type" "License" "Archs"
[13] "Built"
maintainer("MCMCpack")
[1] "Andrew D. Martin "
table(sapply(a[,"Package"],maintainer))
a['glmnet', 'Version']
[1] "1.5.3"# Data sets in package 'datasets'
data()
# list the data sets in all available packages
data(package = .packages(all.available = TRUE))# default packages
getOption("defaultPackages")
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"old.packages()
Package LibPath Installed Built ReposVer
ctv "ctv" "/usr/local/lib/R/site-library" "0.7-0" "2.13.0" "0.7-2"
slam "slam" "/usr/local/lib/R/site-library" "0.1-21" "2.12.2" "0.1-22"
survey "survey" "/usr/local/lib/R/site-library" "3.23-3" "2.13.0" "3.24"
Repository
ctv "http://cran.r-project.org/src/contrib"
slam "http://cran.r-project.org/src/contrib"
survey "http://cran.r-project.org/src/contrib"Read the R-devel post [Rd] function remains loaded in the search space after detachingthe package.
detach(package:lme4, unload=TRUE)remove.packages("packagename")tools::dependsOnPkgs("nlme")
[1] "lme4" "mgcv"
tools::package_dependencies("lme4", available.packages())
$lme4
[1] "methods" "Matrix" "lattice" "graphics" "nlme" "stats4" "stats"
require(packdep)
```r
### Check package version
```r
packageVersion("MCMCglmm")# download source packages and its dependencies (*tar.gz) in /home/gota/R/tmp
# create a repository (create PACKAGES file)
tools::write_PACKAGES("/home/gota/R/tmp", type ="source")
# install
install.packages("xyz.tar.gz", repos=NULL, dependencies= TRUE, type="source", contriburl="file:///home/gota/R/tmp/"))devtools::install_github