[BioC] unable to install lumi package

[Dan Tenenbaum]

Hi,


On Mon, Oct 31, 2011 at 1:12 PM, Juliet Hannah <juliet.hannah at gmail.com> wrote:
> I am unable to install the lumi package. I have printed the output and
> errors below. Below that is my sessionInfo. Other bioconductor
> packages I use installed without any problems. Thanks for any help.
>
>
>> biocLite("lumi")
>
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.1.34.
> Installing package(s) 'lumi'
> also installing the dependencies ârglâ, âksâ, âhdrcdeâ
>
> trying URL 'http://cran.fhcrc.org/src/contrib/rgl_0.92.798.tar.gz'
> Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
>
> trying URL 'http://cran.fhcrc.org/src/contrib/ks_1.8.3.tar.gz'
> Content type 'application/x-gzip' length 283507 bytes (276 Kb)
> opened URL
> ==================================================
> downloaded 276 Kb
>
> trying URL 'http://cran.fhcrc.org/src/contrib/hdrcde_2.15.tar.gz'
> Content type 'application/x-gzip' length 45583 bytes (44 Kb)
> opened URL
> ==================================================
> downloaded 44 Kb
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.5.7.tar.gz'
> Content type 'application/x-gzip' length 11386085 bytes (10.9 Mb)
> opened URL
> ==================================================
> downloaded 10.9 Mb
>
> * installing *source* package ârglâ ...
> checking for gcc... gcc -std=gnu99
> checking for C compiler default output file name... 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 -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for gcc... (cached) gcc -std=gnu99
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc -std=gnu99 accepts -g... (cached) yes
> checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
> checking for libpng-config... yes
> configure: using libpng-config
> configure: using libpng dynamic linkage
> checking for X... libraries , headers
> checking GL/gl.h usability... yes
> checking GL/gl.h presence... yes
> checking for GL/gl.h... yes
> checking GL/glu.h usability... no
> checking GL/glu.h presence... no
> checking for GL/glu.h... no
> configure: error: missing required header GL/glu.h
> ERROR: configuration failed for package ârglâ
> * removing â/home/R-2.14.0/library/rglâ
> ERROR: dependency ârglâ is not available for package âksâ
> * removing âl/home/R-2.14.0/library/ksâ
> ERROR: dependency âksâ is not available for package âhdrcdeâ
> * removing â/home/R-2.14.0/library/hdrcdeâ
> ERROR: dependency âhdrcdeâ is not available for package âlumiâ
> * removing â/home/R-2.14.0/library/lumiâ
>
> The downloaded packages are in
>        â/tmp/Rtmpeyt6CI/downloaded_packagesâ
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ârglâ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package âksâ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package âhdrcdeâ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package âlumiâ had non-zero exit status
>
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-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=C                 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] affy_1.31.6          Biobase_2.13.12      BiocInstaller_1.1.34
>
> loaded via a namespace (and not attached):
> [1] affyio_1.21.2         preprocessCore_1.15.0 tools_2.14.0
> [4] zlibbioc_0.99.0
>

lumi depends on something that depends on the CRAN package rgl.
rgl has some system dependencies, as you can see on its home page:
http://cran.fhcrc.org/web/packages/rgl/index.html

The README for rgl has instructions for configuring your system.
Download the rgl source tarball (the "Package source" link on the page
above), open the tarball and read the README file.

Dan



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