SwimR 1.11.0
Randy Blakely
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SwimR | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | 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-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SwimR_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SwimR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SwimR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwimR’ version ‘1.11.0’
* 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 ‘SwimR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
extdata 4.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘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 to packages already attached by Depends:
‘R2HTML’ ‘gplots’ ‘heatmap.plus’ ‘signal’
Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘R2HTML’ ‘gplots’ ‘heatmap.plus’ ‘methods’ ‘signal’
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
SwimR : remove.outliers: no visible global function definition for
‘median’
SwimR : remove.outliers: no visible global function definition for
‘mad’
SwimR: no visible global function definition for ‘read.table’
SwimR: no visible global function definition for ‘write.table’
SwimR: no visible global function definition for ‘sd’
SwimR: no visible global function definition for ‘jpeg’
SwimR: no visible global function definition for ‘par’
SwimR: no visible global function definition for ‘plot’
SwimR: no visible global function definition for ‘points’
SwimR: no visible global function definition for ‘legend’
SwimR: no visible global function definition for ‘dev.off’
SwimR: no visible binding for global variable ‘sd’
SwimR: no visible global function definition for ‘hist’
SwimR: no visible global function definition for ‘rainbow’
SwimR: no visible global function definition for ‘topo.colors’
SwimR: no visible global function definition for ‘gray’
SwimR: no visible global function definition for ‘colorpanel’
SwimR: no visible global function definition for ‘heatmap.plus’
SwimR: no visible global function definition for ‘HTMLInitFile’
SwimR: no visible global function definition for ‘HTML’
SwimR: no visible global function definition for ‘HTMLEndFile’
SwimR: no visible global function definition for ‘browseURL’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘read.csv’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘fir1’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘as.Arma’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘filter’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘fft’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘hamming’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘jpeg’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘par’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘plot’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘lines’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘legend’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘dev.off’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘layout’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘grid’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
definition for ‘write.csv’
createFrequencyMatrix: no visible global function definition for
‘write.table’
createFrequencyMatrix: no visible global function definition for
‘HTMLInitFile’
createFrequencyMatrix: no visible global function definition for ‘HTML’
createFrequencyMatrix: no visible global function definition for
‘HTMLEndFile’
createFrequencyMatrix: no visible global function definition for
‘browseURL’
Undefined global functions or variables:
HTML HTMLEndFile HTMLInitFile as.Arma browseURL colorpanel dev.off
fft filter fir1 gray grid hamming heatmap.plus hist jpeg layout
legend lines mad median par plot points rainbow read.csv read.table
sd topo.colors write.csv write.table
Consider adding
importFrom("grDevices", "dev.off", "gray", "jpeg", "rainbow",
"topo.colors")
importFrom("graphics", "grid", "hist", "layout", "legend", "lines",
"par", "plot", "points")
importFrom("stats", "fft", "filter", "mad", "median", "sd")
importFrom("utils", "browseURL", "read.csv", "read.table", "write.csv",
"write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createFrequencyMatrix 12.992 0.028 13.018
SwimR 5.200 0.028 5.227
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/SwimR.Rcheck/00check.log’
for details.