Entering edit mode
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 ?rgl?, ?ks?, ?hdrcde?
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
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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
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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
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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
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downloaded 10.9 Mb
* installing *source* package ?rgl? ...
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 ?rgl?
* removing ?/home/R-2.14.0/library/rgl?
ERROR: dependency ?rgl? is not available for package ?ks?
* removing ?l/home/R-2.14.0/library/ks?
ERROR: dependency ?ks? is not available for package ?hdrcde?
* removing ?/home/R-2.14.0/library/hdrcde?
ERROR: dependency ?hdrcde? is not available for package ?lumi?
* removing ?/home/R-2.14.0/library/lumi?
The downloaded packages are in
?/tmp/Rtmpeyt6CI/downloaded_packages?
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ?rgl? had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ?ks? had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ?hdrcde? had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ?lumi? 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