[R] Can't seem to install packages

[Duncan Murdoch]

On 28/05/2015 6:10 AM, Claire Rioualen wrote:
> Hello,
>
> I can't seem to install R packages, since it seemed there were some
> permission problems I "chmoded" /usr/share/R/ and /usr/lib/R/. However,
> there are still errors in the process. Here's my config:
>
> > sessionInfo()
> R version 3.1.1 (2014-07-10)
> 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=en_US.UTF-8    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
>
> other attached packages:
> [1] ggplot2_1.0.1        BiocInstaller_1.16.5
>
> loaded via a namespace (and not attached):
>   [1] colorspace_1.2-6 digest_0.6.8     grid_3.1.1       gtable_0.1.2
>   [5] magrittr_1.5     MASS_7.3-40      munsell_0.4.2    plyr_1.8.2
>   [9] proto_0.3-10     Rcpp_0.11.6      reshape2_1.4.1   scales_0.2.4
> [13] stringi_0.4-1    stringr_1.0.0    tcltk_3.1.1      tools_3.1.1
>
> And here are some packages I tried to install:
>
> *> install.packages("XML")*
> Installing package into ���/packages/rsat/R-scripts/Rpackages���
> (as ���lib��� is unspecified)
> trying URL 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/XML_3.98-1.1.tar.gz'
> Content type 'text/html' length 1582216 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 Mb
>
> * installing *source* package ���XML��� ...
> ** package ���XML��� successfully unpacked and MD5 sums checked
> checking for gcc... gcc
> checking for C compiler default output file name... rm: cannot remove
> 'a.out.dSYM': Is a directory
> a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ���XML���
> * removing ���/packages/rsat/R-scripts/Rpackages/XML���
>
> The downloaded source packages are in
>      ���/tmp/RtmphODjkn/downloaded_packages���
> Warning message:
> In install.packages("XML") :
>    installation of package ���XML��� had non-zero exit status
>
>
> *> install.packages("Biostrings")*
> Installing package into ���/packages/rsat/R-scripts/Rpackages���
> (as ���lib��� is unspecified)
> Warning message:
> package ���Biostrings��� is not available (for R version 3.1.1)
>
> *> biocLite("Biostrings")*
> [...]
> io_utils.c:16:18: fatal error: zlib.h: No such file or directory
>   #include <zlib.h>
>                    ^
> compilation terminated.
> /usr/lib/R/etc/Makeconf:128: recipe for target 'io_utils.o' failed
> make: *** [io_utils.o] Error 1
> ERROR: compilation failed for package ���Biostrings���
> * removing ���/packages/rsat/R-scripts/Rpackages/Biostrings���
>
> The downloaded source packages are in
>      ���/tmp/RtmphODjkn/downloaded_packages���
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package ���Biostrings��� had non-zero exit status
>
>
> I've used R on several machines before and never had such problems.
> Thanks for any clue!
>
It's hard to read your message (I think it was posted in HTML), but I 
think those are all valid errors in building those packages.  You appear 
to be missing some of their dependencies.  This is not likely related to 
permissions.

Duncan Murdoch