[R] Can't seem to install packages

Claire Rioualen claire.rioualen at inserm.fr
Thu May 28 12:10:15 CEST 2015


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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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
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
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
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!

Claire Rioualen
Lab. Technological Advances for Genomics and Clinics (TAGC)
INSERM Unit U1090, Aix-Marseille Université (AMU).
163, Avenue de Luminy,
13288 MARSEILLE cedex 09.

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