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Package 22/389HostnameOS / ArchBUILDCHECKBUILD BIN
altcdfenvs 2.10.0
Laurent Gautier
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/altcdfenvs
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: altcdfenvs
Version: 2.10.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings altcdfenvs_2.10.0.tar.gz
StartedAt: 2010-10-04 15:49:06 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 15:51:49 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 162.2 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'altcdfenvs' 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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: countduplicated.Rd:18-20: Dropping empty section \details
prepare_Rd: countduplicated.Rd:30-31: Dropping empty section \examples
prepare_Rd: index2xy.Rd:26-28: Dropping empty section \details
prepare_Rd: index2xy.Rd:33: Dropping empty section 'Warning '
prepare_Rd: indexProbes.CdfEnvAffy.Rd:35-37: Dropping empty section \examples
prepare_Rd: matchAffyProbes.Rd:46-49: Dropping empty section \note
prepare_Rd: validAffyBatch.Rd:24-26: Dropping empty section \value
* 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 Rd contents ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

altcdfenvs.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'altcdfenvs' ...
** R
** data
** inst
** preparing package for lazy loading

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: AnnotationDbi
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
    rbind, rep.int, table


*** Deprecation warning ***
The matchprobes package is deprecated and will not be supported
anymore starting with Bioconductor 2.4. Please switch to using the
Biostrings package for efficient string manipulations. If you need
to build a probe package, please see the makeProbePackage vignette
in the AnnotationDbi package.

Loading required package: graph

Attaching package: 'graph'

The following object(s) are masked from 'package:Biostrings':

    complement


Attaching package: 'hypergraph'

The following object(s) are masked from 'package:IRanges':

    head, tail

The following object(s) are masked from 'package:AnnotationDbi':

    head, tail

The following object(s) are masked from 'package:utils':

    head, tail

NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for 'toHypergraph' with signature '"CdfEnvAffy"': no definition for class "CdfEnvAffy"
Creating a new generic function for "plot" in "altcdfenvs"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (altcdfenvs)

altcdfenvs.Rcheck/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class0.0000.0000.001
CdfEnvAffy-class7.0840.0047.309
appendCdfEnvAffy0.0040.0000.006
cdfenv000
cdfenvEx0.0000.0040.002
getxy.probeseq0.0000.0000.001
index2xy0.0000.0000.001
matchAffyProbes15.677 0.26815.947
plot.CdfEnvAffy000
removeIndex18.617 0.02818.641
unique.CdfEnvAffy000
utils.FASTA0.0040.0040.007
validAffyBatch000