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BioC 2.13: CHECK report for dyebias on zin1

This page was generated on 2014-04-05 09:47:44 -0700 (Sat, 05 Apr 2014).

Package 216/750HostnameOS / ArchBUILDCHECKBUILD BIN
dyebias 1.20.0
Philip Lijnzaad
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/dyebias
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 [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: dyebias
Version: 1.20.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings dyebias_1.20.0.tar.gz
StartedAt: 2014-04-05 00:53:52 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:54:59 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 67.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: dyebias.Rcheck
Warnings: 2

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/dyebias.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.20.0’
* 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 ‘dyebias’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): object ‘msb.2009.21’ not found
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘marray’
  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 ... NOTE
dyebias.apply.correction: no visible global function definition for
  ‘maR<-’
dyebias.apply.correction: no visible global function definition for
  ‘maG<-’
* checking Rd files ... WARNING
checkRd: (3) dyebias.application.subset.Rd:16-20: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.apply.correction.Rd:10-19: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.boxplot.Rd:17-23: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.estimate.iGSDBs.Rd:12-14: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.rgplot.Rd:17-32: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.trendplot.Rd:22-38: \synopsis will be removed in R 3.1.0
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘dyebias-vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
dyebias.rgplot             6.316  0.024   6.350
dyebias.boxplot            5.909  0.016   5.932
dyebias.trendplot          5.901  0.016   5.959
dyebias.application.subset 5.788  0.080   6.002
dyebias.apply.correction   5.736  0.076   5.827
* 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

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/dyebias.Rcheck/00check.log’
for details.

dyebias.Rcheck/00install.out:

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

dyebias.Rcheck/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset5.7880.0806.002
dyebias.apply.correction5.7360.0765.827
dyebias.boxplot5.9090.0165.932
dyebias.estimate.iGSDBs1.6600.0041.670
dyebias.monotonicity0.0040.0000.007
dyebias.monotonicityplot0.0120.0000.012
dyebias.rgplot6.3160.0246.350
dyebias.trendplot5.9010.0165.959