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On Ubuntu 10.04 I updated a load of the R (ubuntu) packages this morning. Then the first R script I tried told me zoo wasn't built for R 3.0.0. So I do sudo R and then update.packages(ask=F) assuming it would bring all the CRAN packages I've installed over the past couple of years into sync.
But it didn't, and zoo, Rcpp, and more don't work. In fact over half my installed packages are still built for 2.x.x; the list is below (x=installed.packages();x[sort.list(x[,'Built']),c('Built','Version','Depends','LinkingTo','NeedsCompilation')])
Is this tough, not all packages are ready for 3.0.0, and I should (in Ubuntu) revert to the previous version? Or do I need to be using a different CRAN site for 3.x.x? Would deleting all 2.x packages and then installing them fresh again fix it? Or ...?
Built Version Depends LinkingTo NeedsCompilation
Defaults "2.13.1" "1.1-1" NA NA NA
itertools "2.13.1" "0.1-1" "R (>= 2.5.0), iterators(>= 1.0.0)" NA NA
openNLP "2.13.1" "0.0-8" NA NA NA
reshape "2.13.1" "0.8.4" "R (>= 2.6.1), plyr" NA NA
RUnit "2.13.1" "0.4.26" "R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0)" NA NA
multicore "2.14.1" "0.1-7" "R (>= 2.0.0)" NA NA
RMySQL "2.15.0" "0.9-3" "R (>= 2.8.0), methods, DBI (>= 0.2-2), utils" NA NA
foreach "2.15.1" "1.4.0" "R (>= 2.5.0)" NA NA
iterators "2.15.1" "1.0.6" "R (>= 2.5.0), utils" NA NA
labeling "2.15.1" "0.1" NA NA NA
memoise "2.15.1" "0.1" NA NA NA
RColorBrewer "2.15.1" "1.0-5" "R (>= 2.0.0)" NA NA
bitops "2.15.2" "1.0-5" NA NA NA
e1071 "2.15.2" "1.6-1" "class" NA NA
IBrokers "2.15.2" "0.9-10" "xts" NA NA
mgcv "2.15.2" "1.7-22" "R (>= 2.14.0), stats, graphics" NA NA
munsell "2.15.2" "0.4" NA NA NA
randomForest "2.15.2" "4.6-7" "R (>= 2.5.0), stats" NA NA
rbenchmark "2.15.2" "1.0.0" NA NA NA
tree "2.15.2" "1.0-33" "R (>= 2.15.0), grDevices, graphics, stats" NA NA
tseries "2.15.2" "0.10-30" "R (>= 2.10.0)" NA NA
zoo "2.15.2" "1.7-9" "R (>= 2.10.0), stats" NA NA
Cairo "2.15.3" "1.5-2" "R (>= 2.4.0)" NA NA
dichromat "2.15.3" "2.0-0" "R (>= 2.10), stats" NA NA
digest "2.15.3" "0.6.3" "R (>= 2.4.1)" NA "yes"
doMC "2.15.3" "1.3.0" "R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0),\nparallel" NA "no"
FastRWeb "2.15.3" "1.1-0" "R (>= 2.0.0), Cairo" NA NA
forecast "2.15.3" "4.03" "R (>= 2.14.0), stats, graphics" "Rcpp, RcppArmadillo" "yes"
fracdiff "2.15.3" "1.4-2" NA NA NA
ggplot2 "2.15.3" "0.9.3.1" "R (>= 2.14), stats, methods" NA "no"
gtable "2.15.3" "0.1.2" "R (>= 2.14), grid" NA NA
inline "2.15.3" "0.3.11" "R (>= 2.4.0), methods" NA "no"
microbenchmark "2.15.3" "1.3-0" NA NA "yes"
nnet "2.15.3" "7.3-6" "R (>= 2.14.0), stats, utils" NA "yes"
PerformanceAnalytics"2.15.3" "1.1.0" "R (>= 2.14.0), zoo, xts (>= 0.8-9)" NA NA
plyr "2.15.3" "1.8" "R (>= 2.11.0)" NA NA
proto "2.15.3" "0.3-10" NA NA NA
quantmod "2.15.3" "0.4-0" "Defaults, xts(>= 0.9-0), zoo, TTR(>= 0.2), methods" NA NA
Rcpp "2.15.3" "0.10.3" "R (>= 2.15.1)" NA "yes"
RcppArmadillo "2.15.3" "0.3.800.1" "R (>= 2.14.0), Rcpp (>= 0.10.2)" "Rcpp" "yes"
RCurl "2.15.3" "1.95-4.1" "R (>= 2.7.0), methods, bitops" NA "yes"
reshape2 "2.15.3" "1.2.2" NA NA NA
RInside "2.15.3" "0.2.10" "R (>= 2.10.0), Rcpp (>= 0.8.5)" "Rcpp" NA
rJava "2.15.3" "0.9-4" "R (>= 2.5.0), methods" NA "yes"
rjson "2.15.3" "0.2.12" "R (>= 2.12.0)" NA NA
Rserve "2.15.3" "1.7-0" "R (>= 1.5.0)" NA NA
RWeka "2.15.3" "0.4-16" "R (>= 2.6.0)" NA "no"
RWekajars "2.15.3" "3.7.9-1" NA NA "no"
scales "2.15.3" "0.2.3" "R (>= 2.12), methods" NA NA
slam "2.15.3" "0.1-28" "R (>= 2.8.0)" NA NA
stringr "2.15.3" "0.6.2" "R (>= 2.14)" NA NA
tm "2.15.3" "0.5-8.3" "R (>= 2.14.0), methods" NA NA
TTR "2.15.3" "0.22-0" "xts (>= 0.9-3)" "xts" "yes"
XML "2.15.3" "3.96-1.1" "R (>= 1.2.0), methods, utils" NA "yes"
xts "2.15.3" "0.9-3" "zoo (>= 1.7-2)" "zoo (>= 1.7.2)" NA
xtsExtra "2.15.3" "0.0-1" "zoo, xts" NA NA
colorspace "3.0.0" "1.2-2" "R (>= 2.13.0), methods" NA "yes"
DBI "3.0.0" "0.2-7" "R (>= 2.15.0), methods" NA "no"
Hmisc "3.0.0" "3.10-1.1" "R (>= 2.4.0), methods, survival" NA "yes"
quadprog "3.0.0" "1.5-5" "R (>= 2.15.0)" NA "yes"
RSQLite "3.0.0" "0.11.3" "R (>= 2.10.0), methods, DBI (>= 0.2-5)" NA "yes"
base "3.0.0" "3.0.0" NA NA NA
boot "3.0.0" "1.3-9" "R (>= 3.0.0), graphics, stats" NA NA
class "3.0.0" "7.3-7" "R (>= 3.0.0), stats, utils" NA "yes"
cluster "3.0.0" "1.14.4" "R (>= 2.10.0), stats, graphics, utils" NA "yes"
codetools "3.0.0" "0.2-8" "R (>= 2.1)" NA NA
compiler "3.0.0" "3.0.0" NA NA NA
datasets "3.0.0" "3.0.0" NA NA NA
foreign "3.0.0" "0.8-53" "R (>= 2.14.0), stats" NA "yes"
graphics "3.0.0" "3.0.0" NA NA NA
grDevices "3.0.0" "3.0.0" NA NA NA
grid "3.0.0" "3.0.0" NA NA NA
KernSmooth "3.0.0" "2.23-10" "R (>= 2.5.0), stats" NA "yes"
lattice "3.0.0" "0.20-15" "R (>= 2.15.1)" NA "yes"
MASS "3.0.0" "7.3-26" "R (>= 3.0.0), grDevices, graphics, stats, utils" NA "yes"
Matrix "3.0.0" "1.0-12" "R (>= 2.15.0), stats, methods, utils, lattice" NA "yes"
methods "3.0.0" "3.0.0" NA NA NA
mgcv "3.0.0" "1.7-22" "R (>= 2.14.0), stats, graphics" NA NA
nlme "3.0.0" "3.1-109" "graphics, stats, R (>= 3.0.0)" NA NA
nnet "3.0.0" "7.3-6" "R (>= 2.14.0), stats, utils" NA "yes"
parallel "3.0.0" "3.0.0" NA NA NA
rpart "3.0.0" "4.1-1" "R (>= 2.14.0), graphics, stats, grDevices" NA "yes"
spatial "3.0.0" "7.3-6" "R (>= 3.0.0), graphics, stats, utils" NA NA
splines "3.0.0" "3.0.0" NA NA NA
stats "3.0.0" "3.0.0" NA NA NA
stats4 "3.0.0" "3.0.0" "methods, graphics, stats" NA NA
survival "3.0.0" "2.37-4" "stats, utils, graphics, splines, R (>= 2.13.0)" NA "yes"
tcltk "3.0.0" "3.0.0" NA NA NA
tools "3.0.0" "3.0.0" NA NA NA
utils "3.0.0" "3.0.0" NA NA NA
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In code you, can use old. packages() to check to see what packages are out of date. update. packages() will update all packages in the known libraries interactively.
The key thing to be aware of is that when you update R, if you just download the latest version from the website, you will lose all your packages.
Press Ctrl + Left Click or Cmd + Left Click in the function name (written on the script), when using RStudio. Go to the CRAN (or GitHub, R-forge, …) page of the package and download the package file to inspect the source code manually.
The required command is not what you state: update.packages(ask=F) but rather the following update.packages(ask=FALSE, checkBuilt=TRUE).
Try that, and all the still-maintained and available CRAN packages will of course be taken care of. Things you installed from github, Simon's rforge, r-forge, or other random repo will need manual help.
This issue has been discussed at length at various venues since R 3.0.0 came out.
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