AffyExpress 1.37.0
Xuejun Arthur Li
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AffyExpress | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AffyExpress_1.37.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AffyExpress.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.37.0’
* 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 ‘AffyExpress’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘R2HTML’ ‘affyPLM’ ‘annaffy’ ‘gcrma’ ‘genefilter’ ‘simpleaffy’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘affy’ ‘limma’
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
AffyQA: warning in png(file = figure1): partial argument match of
'file' to 'filename'
AffyQA: warning in png(file = figure1, height = 960): partial argument
match of 'file' to 'filename'
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
partial argument match of 'nr' to 'nrow'
AffyQA: warning in png(file = figure2): partial argument match of
'file' to 'filename'
AffyQA: warning in png(file = figure3): partial argument match of
'file' to 'filename'
AffyQA: warning in png(file = figure4): partial argument match of
'file' to 'filename'
AffyQA: warning in png(file = figure5): partial argument match of
'file' to 'filename'
AffyInteraction: no visible global function definition for ‘pData’
AffyInteraction: no visible global function definition for ‘annotation’
AffyInteraction: no visible global function definition for ‘exprs’
AffyQA: no visible global function definition for ‘pData’
AffyQA: no visible global function definition for ‘cdfName’
AffyQA: no visible global function definition for ‘cleancdfname’
AffyQA: no visible global function definition for ‘setQCEnvironment’
AffyQA: no visible global function definition for ‘qc.get.alpha1’
AffyQA: no visible global function definition for ‘HTMLStart’
AffyQA: no visible global function definition for ‘HTML’
AffyQA: no visible global function definition for ‘as.title’
AffyQA: no visible global function definition for ‘HTMLInsertGraph’
AffyQA: no visible global function definition for ‘call.exprs’
AffyQA: no visible global function definition for ‘description’
AffyQA: no visible global function definition for ‘description<-’
AffyQA: no visible global function definition for ‘avbg’
AffyQA: no visible global function definition for ‘percent.present’
AffyQA: no visible global function definition for ‘sfs’
AffyQA: no visible global function definition for ‘spikeInProbes’
AffyQA: no visible global function definition for ‘ratios’
AffyQA: no visible global function definition for ‘AffyRNAdeg’
AffyQA: no visible global function definition for ‘summaryAffyRNAdeg’
AffyQA: no visible global function definition for ‘plotAffyRNAdeg’
AffyQA: no visible global function definition for ‘rma’
AffyQA: no visible global function definition for ‘exprs’
AffyQA: no visible global function definition for ‘sampleNames<-’
AffyQA: no visible global function definition for ‘fitPLM’
AffyQA: no visible global function definition for ‘Mbox’
AffyQA: no visible global function definition for ‘package.version’
AffyQA: no visible global function definition for ‘HTMLStop’
AffyRegress: no visible global function definition for ‘annotation’
AffyRegress: no visible global function definition for ‘pData’
Filter: no visible global function definition for ‘exprs’
Filter: no visible global function definition for ‘kOverA’
Filter: no visible global function definition for ‘filterfun’
Filter: no visible global function definition for ‘genefilter’
f.test: no visible global function definition for ‘classifyTestsF’
get.f: no visible global function definition for ‘classifyTestsF’
import.data: no visible global function definition for
‘read.AnnotatedDataFrame’
import.data: no visible global function definition for ‘ReadAffy’
import.data: no visible global function definition for ‘pData’
interaction.result2html: no visible global function definition for
‘aaf.handler’
interaction.result2html: no visible global function definition for
‘aafTableAnn’
interaction.result2html: no visible global function definition for
‘aafTable’
interaction.result2html: no visible global function definition for
‘saveHTML’
permute.1: no visible global function definition for ‘lmFit’
permute.1: no visible global function definition for ‘contrasts.fit’
post.interaction: no visible global function definition for ‘pData’
pre.process: no visible global function definition for ‘gcrma’
pre.process: no visible global function definition for ‘rma’
pre.process: no visible global function definition for ‘exprs’
regress: no visible global function definition for ‘lmFit’
regress: no visible global function definition for ‘contrasts.fit’
regress: no visible global function definition for ‘eBayes’
result2html: no visible global function definition for ‘aaf.handler’
result2html: no visible global function definition for ‘aafTableAnn’
result2html: no visible global function definition for ‘aafTable’
result2html: no visible global function definition for ‘saveHTML’
Undefined global functions or variables:
AffyRNAdeg HTML HTMLInsertGraph HTMLStart HTMLStop Mbox ReadAffy
aaf.handler aafTable aafTableAnn annotation as.title avbg call.exprs
cdfName classifyTestsF cleancdfname contrasts.fit description
description<- eBayes exprs filterfun fitPLM gcrma genefilter kOverA
lmFit pData package.version percent.present plotAffyRNAdeg
qc.get.alpha1 ratios read.AnnotatedDataFrame rma sampleNames<-
saveHTML setQCEnvironment sfs spikeInProbes summaryAffyRNAdeg
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AffyInteraction 7.071 0.108 7.194
* 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
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/AffyExpress.Rcheck/00check.log’
for details.