[R] Can't seem to install packages

Thu May 28 17:41:10 CEST 2015

Hello,
Indeed I've had a lot of dependencies issues, but I'm solving them one
after the other.
Thanks for your time!

CR

On Thu, May 28, 2015 at 5:33 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> 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
>>
>> ______________________________________________
>> R-help at 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.
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

-- 
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.
France

	[[alternative HTML version deleted]]