ArrayTools 1.30.0
Arthur Li
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ArrayTools | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ArrayTools.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ version ‘1.30.0’
* 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 ‘ArrayTools’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘affy’ ‘Biobase’ ‘methods’
A package should be listed in only one of these fields.
* 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’ ‘simpleaffy’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
createIndex: no visible global function definition for ‘HTMLStart’
createIndex: no visible global function definition for ‘as.title’
createIndex: no visible global function definition for ‘HTML’
createIndex: no visible global function definition for ‘HTMLStop’
geneFilter: no visible global function definition for ‘getText’
geneFilter: no visible global function definition for ‘aafSymbol’
geneFilter: no visible global function definition for ‘aafDescription’
geneFilter: no visible global function definition for ‘aafChromosome’
geneFilter: no visible global function definition for ‘aafGenBank’
geneFilter: no visible global function definition for ‘aafCytoband’
geneFilter: no visible global function definition for ‘aafUniGene’
geneFilter: no visible global function definition for ‘aafPubMed’
geneFilter: no visible global function definition for ‘aafLocusLink’
output.ing: no visible global function definition for ‘getText’
output.ing: no visible global function definition for ‘aafSymbol’
output.ing: no visible global function definition for ‘aafDescription’
output.ing: no visible global function definition for ‘aafChromosome’
output.ing: no visible global function definition for ‘aafGenBank’
output.ing: no visible global function definition for ‘aafCytoband’
output.ing: no visible global function definition for ‘aafUniGene’
output.ing: no visible global function definition for ‘aafPubMed’
output.ing: no visible global function definition for ‘aafLocusLink’
preProcess3prime: no visible global function definition for ‘gcrma’
preProcess3prime: no visible global function definition for ‘getText’
preProcess3prime: no visible global function definition for ‘aafSymbol’
preProcess3prime: no visible global function definition for
‘aafDescription’
preProcess3prime: no visible global function definition for
‘aafChromosome’
preProcess3prime: no visible global function definition for
‘aafGenBank’
preProcess3prime: no visible global function definition for
‘aafCytoband’
preProcess3prime: no visible global function definition for
‘aafUniGene’
preProcess3prime: no visible global function definition for ‘aafPubMed’
preProcess3prime: no visible global function definition for
‘aafLocusLink’
preProcessGeneST: no visible binding for global variable
‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
‘mogene10stCONTROL’
preProcessGeneST: no visible global function definition for ‘getText’
preProcessGeneST: no visible global function definition for ‘aafSymbol’
preProcessGeneST: no visible global function definition for
‘aafDescription’
preProcessGeneST: no visible global function definition for
‘aafChromosome’
preProcessGeneST: no visible global function definition for
‘aafGenBank’
preProcessGeneST: no visible global function definition for
‘aafCytoband’
preProcessGeneST: no visible global function definition for
‘aafUniGene’
preProcessGeneST: no visible global function definition for ‘aafPubMed’
preProcessGeneST: no visible global function definition for
‘aafLocusLink’
qa3prime: no visible global function definition for ‘setQCEnvironment’
qa3prime: no visible global function definition for ‘qc.get.alpha1’
qa3prime: no visible global function definition for ‘HTMLStart’
qa3prime: no visible global function definition for ‘as.title’
qa3prime: no visible global function definition for ‘HTML’
qa3prime: no visible global function definition for ‘HTMLInsertGraph’
qa3prime: no visible global function definition for ‘call.exprs’
qa3prime: no visible global function definition for ‘avbg’
qa3prime: no visible global function definition for ‘percent.present’
qa3prime: no visible global function definition for ‘sfs’
qa3prime: no visible global function definition for ‘spikeInProbes’
qa3prime: no visible global function definition for ‘ratios’
qa3prime: no visible global function definition for ‘fitPLM’
qa3prime: no visible global function definition for ‘HTMLStop’
qaGeneST: no visible global function definition for ‘HTMLStart’
qaGeneST: no visible global function definition for ‘as.title’
qaGeneST: no visible global function definition for ‘HTML’
qaGeneST: no visible global function definition for ‘HTMLInsertGraph’
qaGeneST: no visible global function definition for ‘HTMLStop’
regress: no visible global function definition for ‘permute.1’
regress: no visible binding for global variable ‘design’
Output2HTML,interactionResult : .local: no visible global function
definition for ‘aaf.handler’
Output2HTML,interactionResult : .local: no visible global function
definition for ‘aafTableAnn’
Output2HTML,interactionResult : .local: no visible global function
definition for ‘aafTable’
Output2HTML,interactionResult : .local: no visible global function
definition for ‘saveHTML’
Output2HTML,regressResult : .local: no visible global function
definition for ‘aaf.handler’
Output2HTML,regressResult : .local: no visible global function
definition for ‘aafTableAnn’
Output2HTML,regressResult : .local: no visible global function
definition for ‘aafTable’
Output2HTML,regressResult : .local: no visible global function
definition for ‘saveHTML’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ArrayTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ArrayTools)