affycomp 1.46.0
Rafael A. Irizarry
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affycomp | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affycomp_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/affycomp.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affycomp/DESCRIPTION’ ... OK
* this is package ‘affycomp’ version ‘1.46.0’
* 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 ‘affycomp’ can be installed ... [0m/18m] OK
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
data 7.0Mb
* 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 ‘splines’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘Biobase’ ‘methods’
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
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
l$method.name, add.legend = FALSE, main = main): partial argument
match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
argument match of 'len' to 'length'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
assessDilution: no visible global function definition for ‘exprs’
assessDilution: no visible global function definition for ‘pData’
assessFC: no visible global function definition for ‘exprs’
assessFC: no visible global function definition for ‘pData’
assessFC2: no visible global function definition for ‘exprs’
assessFC2: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘exprs’
assessLS: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘featureNames’
assessMA: no visible global function definition for ‘exprs’
assessMA: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘exprs’
assessMA2: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘featureNames’
assessSD: no visible global function definition for ‘exprs’
assessSD: no visible global function definition for ‘assayDataElement’
assessSD: no visible global function definition for ‘pData’
assessSignal: no visible global function definition for ‘exprs’
assessSignal: no visible global function definition for ‘pData’
assessSignal: no visible global function definition for ‘featureNames’
assessSpikeIn2: no visible global function definition for ‘exprs’
assessSpikeInSD: no visible global function definition for ‘pData’
assessSpikeInSD: no visible global function definition for
‘featureNames’
assessSpikeInSD: no visible global function definition for ‘esApply’
exprset.log: no visible global function definition for ‘exprs’
exprset.log: no visible global function definition for ‘exprs<-’
read.dilution: no visible global function definition for ‘sampleNames’
read.spikein: no visible global function definition for ‘sampleNames’
remove.hgu133a.xhyb: no visible global function definition for
‘featureNames’
* 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 ... [5s/202s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SD 0.836 0.227 58.032
affycompPlot 0.898 0.071 25.725
affycomp.compfigs.auxiliary 0.640 0.322 92.517
affycomp.figures.auxiliary 0.542 0.059 21.598
* 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/affycomp.Rcheck/00check.log’
for details.