ITALICS 2.11.1
Guillem Rigaill
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ITALICS | | Last Changed Rev: 52476 / Revision: 53825 | | Last Changed Date: 2011-02-04 15:34:50 -0800 (Fri, 04 Feb 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | ERROR | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | [ ERROR ] | skipped | skipped |
* checking for file 'ITALICS/DESCRIPTION' ... OK
* preparing 'ITALICS':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: ITALICS
Loading required package: GLAD
######################################################################################
Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002)
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008)
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
######################################################################################
New options are available in daglad: see help for details.
Loading required package: ITALICSData
Loading required package: oligo
Loading required package: oligoClasses
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")'.
================================================================================
Welcome to oligoClasses version 1.13.18
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.15.4
================================================================================
Loading required package: affxparser
Loading required package: pd.mapping50k.xba240
Loading required package: RSQLite
Loading required package: DBI
Welcome to ITALICS
#################################################################################################
# This implementation of the ITALICS algorithm was developped for bioconductor
# This implementation is sligthly different
than the original one which is available at :
# http://xfer.curie.fr/get/Zsx2xwOnH2l/ITALICSData_0.0.2.tar.gz
and# http://xfer.curie.fr/get/diXljlXCEev/ITALICS_0.1.0.tar.gz
#################################################################################################
# The two main functions of the package are ITALICS and trainITALICS
# ITALICS : See the help of the ITALICS function (?ITALICS) or read the vignette vignette to see how to normalize
# using ITALICS.
#
# trainITALICS : See the help of the trainITALICS function (?trainITALICS)
#################################################################################################
Warning in file(file, "rt") :
cannot open file '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/ITALICSData/data/Xba.QuartetEffect.csv': No such file or directory
Error: processing vignette 'ITALICS.Rnw' failed with diagnostics:
chunk 2
Error in file(file, "rt") : cannot open the connection
Execution halted