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Package 177/353HostnameOS / ArchBUILDCHECKBUILD BIN
ITALICS 2.6.0
Guillem Rigaill
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/ITALICS
Last Changed Rev: 42684 / Revision: 43539
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: ITALICS
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD check --no-vignettes ITALICS_2.6.0.tar.gz
StartedAt: 2009-12-14 05:59:49 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 06:02:10 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 141.5 seconds
RetCode: 0
Status: OK
CheckDir: ITALICS.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/ITALICS.Rcheck'
* using R version 2.10.0 Patched (2009-10-27 r50222)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ITALICS/DESCRIPTION' ... OK
* this is package 'ITALICS' version '2.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ITALICS' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: GLAD.GLAD.Rd:33: Dropping empty section \keyword
prepare_Rd: ITALICSNew.Rd:82: Dropping empty section \keyword
prepare_Rd: ITALICSTrain.Rd:43: Dropping empty section \keyword
prepare_Rd: Model.GetConfDat.Rd:23: Dropping empty section \keyword
prepare_Rd: Model.GetCorrection.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetEffet.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetModel.Rd:21: Dropping empty section \keyword
prepare_Rd: Model.GetResidu.Rd:18: Dropping empty section \keyword
prepare_Rd: New.AddInfo.Rd:24: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:31: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:25: Dropping empty section \examples
prepare_Rd: New.fromSnpToQuartet.Rd:25: Dropping empty section \keyword
prepare_Rd: New.getQuartet.Rd:27: Dropping empty section \keyword
prepare_Rd: New.getSnpInfo.Rd:25: Dropping empty section \keyword
prepare_Rd: New.readQuartetCopyNb.Rd:23: Dropping empty section \keyword
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

ITALICS.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘ITALICS’ ...
** R
** inst
** preparing package for lazy loading

######################################################################################

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: oligoClasses
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: preprocessCore
Welcome to oligo version 1.10.0
Loading required package: RSQLite
Loading required package: DBI
** help
*** installing help indices
** building package indices ...
* DONE (ITALICS)