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BioC 2.13: CHECK report for DeconRNASeq on perceval

This page was generated on 2014-04-05 09:52:56 -0700 (Sat, 05 Apr 2014).

Package 193/750HostnameOS / ArchBUILDCHECKBUILD BIN
DeconRNASeq 1.4.0
Ting Gong
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/DeconRNASeq
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: DeconRNASeq
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DeconRNASeq_1.4.0.tar.gz
StartedAt: 2014-04-05 00:43:35 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:44:46 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 71.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DeconRNASeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/DeconRNASeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeconRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeconRNASeq’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DeconRNASeq’ can be installed ... [6s/6s] OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘pcaMethods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DeconRNASeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/DeconRNASeq.Rcheck/00check.log’
for details.

DeconRNASeq.Rcheck/00install.out:

* installing *source* package ‘DeconRNASeq’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DeconRNASeq)

DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings:

nameusersystemelapsed
DeconRNASeq0.0090.0010.010
all.datasets0.2670.0120.280
array.proportions0.2260.0120.237
array.signatures0.2440.0080.252
condplot0.2440.0080.252
datasets0.1250.0140.139
fraction0.4690.0250.494
liver_kidney0.1090.0110.120
multi_tissue0.2940.0310.326
multiplot0.0130.0080.021
proportions0.0980.0140.112
signatures0.1100.0210.133
x.data0.3190.0310.351
x.signature0.4230.0290.452
x.signature.filtered0.4380.0330.470
x.signature.filtered.optimal0.2940.0250.320