[R] Can't seem to install packages

[Martin Morgan]

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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