Error installing R 2.13.0 packages (caret) on Ubuntu 10.04

Question

I have R installed via the CRAN repo as instructed at http://cran.r-project.org/bin/linux/ubuntu/. I've been able to install caret fine on a couple other identical Ubuntu 10.04 systems in the past, but today install.packages('caret', dependencies=c('Depends','Suggests')) resulted in the following errors (just a sample). Any hints?

...
** testing if installed package can be loaded

* DONE (dynlm)
ERROR: dependencies ‘reshape’, ‘plyr’, ‘digest’ are not available for package ‘ggplot2’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/ggplot2’
ERROR: dependencies ‘digest’, ‘stringr’, ‘mutatr’, ‘evaluate’ are not available for package ‘testthat’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/testthat’
* installing *source* package ‘ROCR’ ...
** R
...
** testing if installed package can be loaded

* DONE (ROCR)
ERROR: dependencies ‘plyr’, ‘stringr’ are not available for package ‘reshape2’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/reshape2’
* installing *source* package ‘party’ ...
** libs
...
** testing if installed package can be loaded

* DONE (party)
ERROR: dependencies ‘reshape’, ‘plyr’ are not available for package ‘caret’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/caret’
* installing *source* package ‘rocc’ ...
** R
...
* DONE (rocc)
ERROR: dependency ‘reshape2’ is not available for package ‘Cubist’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Cubist’

The downloaded packages are in
        ‘/tmp/Rtmp2TsElZ/downloaded_packages’
There were 20 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'Rmpi' had non-zero exit status
2: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'rpvm' had non-zero exit status
3: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'rsprng' had non-zero exit status
4: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'XML' had non-zero exit status
5: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'RODBC' had non-zero exit status
6: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'rgl' had non-zero exit status
7: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'RWeka' had non-zero exit status
8: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'shapes' had non-zero exit status
9: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'rgeos' had non-zero exit status
10: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'rgdal' had non-zero exit status
11: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'plyr' had non-zero exit status
12: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'stringr' had non-zero exit status
13: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'latentnet' had non-zero exit status
14: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'reshape' had non-zero exit status
15: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'statnet' had non-zero exit status
16: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'ggplot2' had non-zero exit status
17: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'testthat' had non-zero exit status
18: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'reshape2' had non-zero exit status
19: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'caret' had non-zero exit status
20: In install.packages("caret", dependencies = c("Depends",  ... :
  installation of package 'Cubist' had non-zero exit status
> library(caret)
Error in library(caret) : there is no package called 'caret'

> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.13.0
> install.packages('caret', dependencies=c('Depends','Suggests')) # run again
...
ERROR: dependencies ‘digest’, ‘stringr’, ‘mutatr’, ‘evaluate’ are not available for package ‘testthat’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/testthat’
ERROR: dependency ‘itertools’ is not available for package ‘plyr’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/plyr’
ERROR: dependencies ‘RWekajars’, ‘rJava’ are not available for package ‘RWeka’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/RWeka’
ERROR: dependencies ‘plyr’, ‘stringr’ are not available for package ‘reshape2’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/reshape2’
ERROR: dependency ‘plyr’ is not available for package ‘reshape’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/reshape’
ERROR: dependency ‘reshape2’ is not available for package ‘Cubist’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Cubist’
ERROR: dependencies ‘reshape’, ‘plyr’ are not available for package ‘caret’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/caret’
...

Answer 1

Do you have the correct sets of development packages on your Ubuntu box? I would start working down the list of packages that failed and try to install them one by one using install.packages(). I know some of those packages that failed need plenty of development headers against which the R package is compiled.

If you do these one at a time, you'll start to see why packages were failing. I use Fedora, but for rgdal for example, have gdal-devel and proj-devel, proj-epsg and proj-nad installed from my distro's package manager in order to compile that R package. For XML I needed to have libxml2-devel installed, etc. If you step through the R packages that failed, it should become obvious which headers were missing and you can use your package manager to find which Ubuntu package (debs) you need to install to get those headers.