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POR 3.0.0 update has left loads of 2.x packages incompatible
 

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  1. POR 3.0.0 update has left loads of 2.x packages incompatible
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    <p>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 <code>sudo R</code> and then <code>update.packages(ask=F)</code> assuming it would bring all the CRAN packages I've installed over the past couple of years into sync.</p> <p>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 (<code>x=installed.packages();x[sort.list(x[,'Built']),c('Built','Version','Depends','LinkingTo','NeedsCompilation')]</code>)</p> <p>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 ...?</p> <pre><code> Built Version Depends LinkingTo NeedsCompilation Defaults "2.13.1" "1.1-1" NA NA NA itertools "2.13.1" "0.1-1" "R (&gt;= 2.5.0), iterators(&gt;= 1.0.0)" NA NA openNLP "2.13.1" "0.0-8" NA NA NA reshape "2.13.1" "0.8.4" "R (&gt;= 2.6.1), plyr" NA NA RUnit "2.13.1" "0.4.26" "R (&gt;= 2.5.0), utils (&gt;= 2.5.0), methods (&gt;= 2.5.0)" NA NA multicore "2.14.1" "0.1-7" "R (&gt;= 2.0.0)" NA NA RMySQL "2.15.0" "0.9-3" "R (&gt;= 2.8.0), methods, DBI (&gt;= 0.2-2), utils" NA NA foreach "2.15.1" "1.4.0" "R (&gt;= 2.5.0)" NA NA iterators "2.15.1" "1.0.6" "R (&gt;= 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 (&gt;= 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 (&gt;= 2.14.0), stats, graphics" NA NA munsell "2.15.2" "0.4" NA NA NA randomForest "2.15.2" "4.6-7" "R (&gt;= 2.5.0), stats" NA NA rbenchmark "2.15.2" "1.0.0" NA NA NA tree "2.15.2" "1.0-33" "R (&gt;= 2.15.0), grDevices, graphics, stats" NA NA tseries "2.15.2" "0.10-30" "R (&gt;= 2.10.0)" NA NA zoo "2.15.2" "1.7-9" "R (&gt;= 2.10.0), stats" NA NA Cairo "2.15.3" "1.5-2" "R (&gt;= 2.4.0)" NA NA dichromat "2.15.3" "2.0-0" "R (&gt;= 2.10), stats" NA NA digest "2.15.3" "0.6.3" "R (&gt;= 2.4.1)" NA "yes" doMC "2.15.3" "1.3.0" "R (&gt;= 2.14.0), foreach(&gt;= 1.2.0), iterators(&gt;= 1.0.0),\nparallel" NA "no" FastRWeb "2.15.3" "1.1-0" "R (&gt;= 2.0.0), Cairo" NA NA forecast "2.15.3" "4.03" "R (&gt;= 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 (&gt;= 2.14), stats, methods" NA "no" gtable "2.15.3" "0.1.2" "R (&gt;= 2.14), grid" NA NA inline "2.15.3" "0.3.11" "R (&gt;= 2.4.0), methods" NA "no" microbenchmark "2.15.3" "1.3-0" NA NA "yes" nnet "2.15.3" "7.3-6" "R (&gt;= 2.14.0), stats, utils" NA "yes" PerformanceAnalytics"2.15.3" "1.1.0" "R (&gt;= 2.14.0), zoo, xts (&gt;= 0.8-9)" NA NA plyr "2.15.3" "1.8" "R (&gt;= 2.11.0)" NA NA proto "2.15.3" "0.3-10" NA NA NA quantmod "2.15.3" "0.4-0" "Defaults, xts(&gt;= 0.9-0), zoo, TTR(&gt;= 0.2), methods" NA NA Rcpp "2.15.3" "0.10.3" "R (&gt;= 2.15.1)" NA "yes" RcppArmadillo "2.15.3" "0.3.800.1" "R (&gt;= 2.14.0), Rcpp (&gt;= 0.10.2)" "Rcpp" "yes" RCurl "2.15.3" "1.95-4.1" "R (&gt;= 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 (&gt;= 2.10.0), Rcpp (&gt;= 0.8.5)" "Rcpp" NA rJava "2.15.3" "0.9-4" "R (&gt;= 2.5.0), methods" NA "yes" rjson "2.15.3" "0.2.12" "R (&gt;= 2.12.0)" NA NA Rserve "2.15.3" "1.7-0" "R (&gt;= 1.5.0)" NA NA RWeka "2.15.3" "0.4-16" "R (&gt;= 2.6.0)" NA "no" RWekajars "2.15.3" "3.7.9-1" NA NA "no" scales "2.15.3" "0.2.3" "R (&gt;= 2.12), methods" NA NA slam "2.15.3" "0.1-28" "R (&gt;= 2.8.0)" NA NA stringr "2.15.3" "0.6.2" "R (&gt;= 2.14)" NA NA tm "2.15.3" "0.5-8.3" "R (&gt;= 2.14.0), methods" NA NA TTR "2.15.3" "0.22-0" "xts (&gt;= 0.9-3)" "xts" "yes" XML "2.15.3" "3.96-1.1" "R (&gt;= 1.2.0), methods, utils" NA "yes" xts "2.15.3" "0.9-3" "zoo (&gt;= 1.7-2)" "zoo (&gt;= 1.7.2)" NA xtsExtra "2.15.3" "0.0-1" "zoo, xts" NA NA colorspace "3.0.0" "1.2-2" "R (&gt;= 2.13.0), methods" NA "yes" DBI "3.0.0" "0.2-7" "R (&gt;= 2.15.0), methods" NA "no" Hmisc "3.0.0" "3.10-1.1" "R (&gt;= 2.4.0), methods, survival" NA "yes" quadprog "3.0.0" "1.5-5" "R (&gt;= 2.15.0)" NA "yes" RSQLite "3.0.0" "0.11.3" "R (&gt;= 2.10.0), methods, DBI (&gt;= 0.2-5)" NA "yes" base "3.0.0" "3.0.0" NA NA NA boot "3.0.0" "1.3-9" "R (&gt;= 3.0.0), graphics, stats" NA NA class "3.0.0" "7.3-7" "R (&gt;= 3.0.0), stats, utils" NA "yes" cluster "3.0.0" "1.14.4" "R (&gt;= 2.10.0), stats, graphics, utils" NA "yes" codetools "3.0.0" "0.2-8" "R (&gt;= 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 (&gt;= 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 (&gt;= 2.5.0), stats" NA "yes" lattice "3.0.0" "0.20-15" "R (&gt;= 2.15.1)" NA "yes" MASS "3.0.0" "7.3-26" "R (&gt;= 3.0.0), grDevices, graphics, stats, utils" NA "yes" Matrix "3.0.0" "1.0-12" "R (&gt;= 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 (&gt;= 2.14.0), stats, graphics" NA NA nlme "3.0.0" "3.1-109" "graphics, stats, R (&gt;= 3.0.0)" NA NA nnet "3.0.0" "7.3-6" "R (&gt;= 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 (&gt;= 2.14.0), graphics, stats, grDevices" NA "yes" spatial "3.0.0" "7.3-6" "R (&gt;= 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 (&gt;= 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 </code></pre>
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      1. USDave Kincaid
      1. VTFavorite
    1. COBTW There are 110 packages on CRAN that depend on Rcpp, and they all work with R 2.15.* _and_ R 3.0.0, but you need to properly take care of things at your end.
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      1. USDirk Eddelbuettel
    2. COAs an aside: using `sudo` is probably not a great idea; it would be better to make yourself a member of the group that owns the library directory.
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      1. USGSee
    3. COYou may want to get rid of a few of your columns so that the important column (far right) is easier to find (not needing to scroll). I missed it first time looking at this post.
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      1. POR 3.0.0 update has left loads of 2.x packages incompatible
      1. USClayton Stanley
 

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