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Old 12-31-2011, 10:24 AM   #1
crh
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Location: tx

Join Date: Dec 2009
Posts: 46
Default DESeq: problem updating to new version

Hi All,

I attempted to upgrade DESeq to the new version and received an error that I was missing library 'xtable'.

I checked cran and the link to xtable is dead.
This is on a Mac 10.6.8
Suggestions?




installing *source* package ‘DESeq’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c pval.c -o pval.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq/libs/i386
*** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c pval.c -o pval.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq/libs/x86_64
** R
** inst
** preparing package for lazy loading
locfit 1.5-6 2010-01-20
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
there is no package called ‘xtable’
ERROR: lazy loading failed for package ‘DESeq’
* removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq’

The downloaded packages are in
‘/private/var/folders/eM/eMuaz8lA2RayeU+BYvAbo++++TI/-Tmp-/RtmpsnWPGf/downloaded_packages’
> library("DESeq")
Loading required package: Biobase

Welcome to Bioconductor

Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 2010-01-20
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
there is no package called ‘xtable’
In addition: Warning message:
In install.packages(c("DESeq"), lib = "/Library/Frameworks/R.framework/Resources/library/", :
installation of package ‘DESeq’ had non-zero exit status
Error: package/namespace load failed for ‘DESeq’
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] locfit_1.5-6 lattice_0.20-0 akima_0.5-4 Biobase_2.14.0

loaded via a namespace (and not attached):
[1] grid_2.14.0 tools_2.14.0
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Old 01-02-2012, 11:47 PM   #2
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
Default

First: Well, have you tried installing the xtable package?

Second: If you use the proper Bioconductor install script, as described here, such dependencies will be resolved automatically for you.
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