On 05/28/2015 08:21 AM, Duncan Murdoch wrote:
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���
this is a missing system dependency, requiring the libxml2 'dev' headers. On my
linux this is
sudo apt-get installl libxml2-dev
likely you'll also end up needing curl via libcurl4-openssl-dev or similar
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")*
Yes,Bioconductor versions packages differently from CRAN (we have twice-yearly
releases and stable 'release' and 'devel' branches). Following the instructions
for package installation at
http://bioconductor.org/packages/Biostrings
but...
[...]
io_utils.c:16:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
this seems like a relatively basic header to be missing, installable from
zlib1g-dev, but I wonder if you're taking a mis-step earlier, e.g., trying to
install on a cluster node that is configured for software use but not installation?
Also the instructions here to install R
http://cran.r-project.org/bin/linux/
would likely include these basic dependencies 'out of the box'.
Martin
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
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______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
