[BioC] unable to install lumi package

[James W. MacDonald]

Hi Juliet,

On 10/31/2011 4:12 PM, Juliet Hannah 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

Looks like you are missing the GL headers. You want to install the 
mesa-libGLU-devel rpm, using yum or apt, depending on your distro (or 
have your sysadmin do it if you don't have root privileges).

See for instance

http://fedoraforum.org/forum/showthread.php?t=243265

Best,

Jim


> 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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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