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BioC 3.4: CHECK report for coRNAi on malbec1

This page was generated on 2017-04-15 16:10:07 -0400 (Sat, 15 Apr 2017).

Package 266/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRNAi 1.24.0
Elin Axelsson
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/coRNAi
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coRNAi
Version: 1.24.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings coRNAi_1.24.0.tar.gz
StartedAt: 2017-04-14 21:49:46 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:52:02 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 135.9 seconds
RetCode: 0
Status:  OK 
CheckDir: coRNAi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings coRNAi_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/coRNAi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coRNAi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coRNAi’ 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 ‘coRNAi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘cellHTS2’ ‘limma’ ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘moMatrix’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BoxPlotShorth: no visible binding for global variable ‘shorth’
InteractLevelPlot: no visible global function definition for ‘plot’
MAplot: no visible global function definition for ‘plot’
MainFitPlot: no visible global function definition for ‘plot’
MainFitPlot: no visible global function definition for ‘locfit’
MainFitPlot: no visible global function definition for ‘lfknots’
MainFitPlot: no visible global function definition for ‘predict’
MainFitPlot: no visible global function definition for ‘lines’
PlotGraph: no visible global function definition for ‘plot’
Pplot: no visible global function definition for ‘plot’
SDplot: no visible global function definition for ‘plot’
WithinScreenPlot: no visible global function definition for ‘plot’
cellHTS2df: no visible global function definition for ‘fData’
cellHTS2df: no visible global function definition for ‘Data’
df2lmFit: no visible global function definition for ‘lmFit’
estpart: no visible binding for global variable ‘shorth’
interactiontable: no visible global function definition for ‘topTable’
interactiontable: no visible global function definition for ‘eBayes’
lmpart: no visible global function definition for ‘coef’
rlmpart: no visible global function definition for ‘coef’
Undefined global functions or variables:
  Data coef eBayes fData lfknots lines lmFit locfit plot predict shorth
  topTable
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "coef", "predict")
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 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 ... 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-3.4-bioc/meat/coRNAi.Rcheck/00check.log’
for details.


coRNAi.Rcheck/00install.out:

* installing *source* package ‘coRNAi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (coRNAi)

coRNAi.Rcheck/coRNAi-Ex.timings:

nameusersystemelapsed
BoxPlotShorth0.1040.0040.105
InteractGraph0.0000.0000.001
InteractLevelPlot0.1920.0000.193
MainFitPlot0.0160.0000.015
PlotHeatmap0.4040.0000.405
Pplot0.0040.0000.003
cellHTS2df0.0560.0000.056
cortestmatrices2.9320.0122.948
data2graph000
df2array0.0480.0000.049
df2fitmatrix0.0760.0000.076
df2lmFit0.0960.0000.096
estmodel0.0560.0040.063
faultyscreen0.0640.0000.065
interactiontable0.0120.0000.013
key0.0000.0000.003
repplots3.7440.0643.810
rlmmain0.0920.0000.091
screen1_raw0.0120.0000.010
screen2_raw0.0880.0000.087
signalplots0.0800.0000.081
tt2matrix0.0000.0000.002
updateDf0.0680.0000.066
weightDf0.0520.0000.053