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BioC 3.5: CHECK report for ARRmNormalization on veracruz2

This page was generated on 2017-08-16 13:30:51 -0400 (Wed, 16 Aug 2017).

Package 67/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ARRmNormalization 1.16.0
Jean-Philippe Fortin
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ARRmNormalization
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ARRmNormalization
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ARRmNormalization_1.16.0.tar.gz
StartedAt: 2017-08-15 23:50:25 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:52:11 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 106.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ARRmNormalization_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ARRmNormalization.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ARRmNormalization/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ARRmNormalization’ version ‘1.16.0’
* 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 ‘ARRmNormalization’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ARRmData’
  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
ARRm.regression: no visible global function definition for ‘C’
ARRm.regression: no visible global function definition for ‘lm’
getBackground : <anonymous>: no visible global function definition for
  ‘median’
getQuantiles: no visible global function definition for ‘data’
getQuantiles: no visible binding for global variable ‘ProbesType’
getQuantiles : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeARRm: no visible global function definition for ‘data’
normalizeARRm: no visible binding for global variable ‘ProbesType’
normalizeI: no visible global function definition for ‘C’
normalizeI: no visible global function definition for ‘median’
normalizeI : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeI: no visible global function definition for ‘smooth.spline’
normalizeI: no visible global function definition for ‘predict’
normalizeII: no visible global function definition for ‘C’
normalizeII: no visible global function definition for ‘median’
normalizeII : <anonymous>: no visible global function definition for
  ‘quantile’
normalizeII: no visible global function definition for ‘smooth.spline’
normalizeII: no visible global function definition for ‘predict’
positionPlots: no visible global function definition for ‘pdf’
positionPlots: no visible global function definition for ‘plot’
positionPlots: no visible global function definition for ‘axis’
positionPlots: no visible global function definition for ‘abline’
positionPlots: no visible global function definition for ‘dev.off’
quantilePlots: no visible global function definition for ‘pdf’
quantilePlots: no visible global function definition for ‘plot’
quantilePlots: no visible global function definition for ‘points’
quantilePlots: no visible global function definition for ‘abline’
quantilePlots: no visible global function definition for ‘lm’
quantilePlots: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  C ProbesType abline axis data dev.off lm median pdf plot points
  predict quantile smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "C", "lm", "median", "predict", "quantile",
             "smooth.spline")
  importFrom("utils", "data")
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
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeARRm   26.516  6.257  33.718
getCoefficients 12.684  1.369  14.381
positionPlots    9.982  1.552  11.837
getQuantiles     9.789  1.487  11.539
quantilePlots    9.111  1.482  10.900
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ARRmNormalization.Rcheck/00check.log’
for details.


ARRmNormalization.Rcheck/00install.out:

* installing *source* package ‘ARRmNormalization’ ...
** 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 (ARRmNormalization)

ARRmNormalization.Rcheck/ARRmNormalization-Ex.timings:

nameusersystemelapsed
ProbesType0.9560.0361.028
getBackground0.0630.0040.068
getCoefficients12.684 1.36914.381
getDesignInfo0.0050.0010.006
getQuantiles 9.789 1.48711.539
normalizeARRm26.516 6.25733.718
positionPlots 9.982 1.55211.837
quantilePlots 9.111 1.48210.900