dyebias 1.24.0
Philip Lijnzaad
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/dyebias | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings dyebias_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/dyebias.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.24.0’
* 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 ... 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' calls in package code:
‘limma’ ‘methods’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.check.reporter.labels: no visible global function definition for
‘maLabels’
.check.reporter.labels: no visible global function definition for
‘maGnames’
.check.reporter.labels: no visible global function definition for
‘maNspots’
.check.slide.labels: no visible global function definition for
‘maNsamples’
.check.slide.labels: no visible global function definition for
‘maLabels’
.check.slide.labels: no visible global function definition for
‘maTargets’
.limma.to.dataframe: no visible global function definition for ‘eBayes’
.merge.dyebias: no visible global function definition for ‘maLabels’
.merge.dyebias: no visible global function definition for ‘maGnames’
.monotonicity: no visible global function definition for ‘maNsamples’
.monotonicity : <anonymous>: no visible global function definition for
‘maM’
.set.design: no visible global function definition for ‘modelMatrix’
.set.design : <anonymous>: no visible global function definition for
‘modelMatrix’
.slide.bias: no visible global function definition for ‘maNsamples’
.slide.bias: no visible global function definition for ‘maLabels’
.slide.bias: no visible global function definition for ‘maTargets’
.slide.bias: no visible global function definition for ‘maM’
dyebias.application.subset: no visible global function definition for
‘maInfo’
dyebias.application.subset: no visible global function definition for
‘maTargets’
dyebias.application.subset: no visible global function definition for
‘maNspots’
dyebias.application.subset: no visible global function definition for
‘maNsamples’
dyebias.application.subset: no visible global function definition for
‘maRb’
dyebias.application.subset: no visible global function definition for
‘maGb’
dyebias.application.subset: no visible global function definition for
‘maRf’
dyebias.application.subset: no visible global function definition for
‘maGf’
dyebias.apply.correction: no visible global function definition for
‘maM’
dyebias.apply.correction: no visible global function definition for
‘maNspots’
dyebias.apply.correction: no visible global function definition for
‘maNsamples’
dyebias.apply.correction: no visible global function definition for
‘maLabels’
dyebias.apply.correction: no visible global function definition for
‘maGnames’
dyebias.apply.correction: no visible global function definition for
‘maInfo’
dyebias.apply.correction: no visible global function definition for
‘maTargets’
dyebias.apply.correction: no visible global function definition for
‘maA’
dyebias.apply.correction: no visible global function definition for
‘maM<-’
dyebias.apply.correction: no visible global function definition for
‘maA<-’
dyebias.apply.correction: no visible global function definition for
‘maR<-’
dyebias.apply.correction: no visible global function definition for
‘maG<-’
dyebias.boxplot: no visible global function definition for ‘maNsamples’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maLabels’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maGnames’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maNspots’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maNsamples’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maM’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maA’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maInfo’
dyebias.estimate.iGSDBs: no visible global function definition for
‘maTargets’
dyebias.estimate.iGSDBs: no visible global function definition for
‘lmFit’
dyebias.estimate.iGSDBs: no visible global function definition for
‘eBayes’
dyebias.maplot: no visible global function definition for ‘maM’
dyebias.maplot: no visible global function definition for ‘maA’
dyebias.rgplot: no visible global function definition for ‘maA’
dyebias.rgplot: no visible global function definition for ‘maM’
dyebias.trendplot: no visible global function definition for
‘maNsamples’
dyebias.trendplot : <anonymous>: no visible global function definition
for ‘maM’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] 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
* DONE
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/dyebias.Rcheck/00check.log’
for details.