BioC 3.5: CHECK report for coRNAi on oaxaca

Package: coRNAi

Version: 1.25.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coRNAi_1.25.2.tar.gz

StartedAt: 2017-03-04 01:15:03 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:17:36 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 152.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: coRNAi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coRNAi_1.25.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/coRNAi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.25.2’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'coRNAi' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/coRNAi.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/coRNAi.Rcheck/00check.log’
for details.

* 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
Warning: Package 'coRNAi' is deprecated and will be removed from Bioconductor
  version 3.6
* DONE (coRNAi)

name	user	system	elapsed
BoxPlotShorth	0.119	0.006	0.125
InteractGraph	0	0	0
InteractLevelPlot	0.287	0.029	0.316
MainFitPlot	0.462	0.002	0.509
PlotHeatmap	0.330	0.007	0.337
Pplot	0.003	0.000	0.004
cellHTS2df	0.088	0.006	0.094
cortestmatrices	4.331	0.092	4.425
data2graph	0.001	0.000	0.000
df2array	0.069	0.008	0.076
df2fitmatrix	0.098	0.010	0.109
df2lmFit	0.206	0.010	0.216
estmodel	0.174	0.006	0.180
faultyscreen	0.097	0.006	0.104
interactiontable	0.797	0.003	0.801
key	0.004	0.002	0.005
repplots	3.582	0.239	3.849
rlmmain	0.121	0.014	0.137
screen1_raw	0.011	0.002	0.013
screen2_raw	0.126	0.006	0.132
signalplots	0.132	0.009	0.155
tt2matrix	0.002	0.001	0.002
updateDf	0.088	0.006	0.095
weightDf	0.081	0.006	0.087