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BioC 3.5: CHECK report for OperaMate on veracruz2

This page was generated on 2017-08-16 13:33:19 -0400 (Wed, 16 Aug 2017).

Package 927/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OperaMate 1.8.0
Chenglin Liu
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/OperaMate
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: OperaMate
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OperaMate_1.8.0.tar.gz
StartedAt: 2017-08-16 06:08:48 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:11:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 138.9 seconds
RetCode: 0
Status:  OK 
CheckDir: OperaMate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OperaMate_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/OperaMate.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 ‘OperaMate/DESCRIPTION’ ... OK
* this is package ‘OperaMate’ version ‘1.8.0’
* 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 ‘OperaMate’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cellData: no visible global function definition for ‘combn’
cellSigAnalysis: no visible global function definition for
  ‘write.table’
cellSigPlot: no visible binding for global variable ‘strwidth’
cellSigPlot: no visible binding for global variable ‘strheight’
fitStable: no visible global function definition for ‘abline’
generateReport: no visible global function definition for ‘write.table’
operaMate : configParser: no visible global function definition for
  ‘read.csv’
parseFullTab: no visible global function definition for ‘read.delim’
parseMatrix: no visible global function definition for ‘read.delim’
parseTab: no visible global function definition for ‘read.delim’
wellQC : <anonymous>: no visible global function definition for
  ‘boxplot’
wellQC: no visible global function definition for ‘boxplot’
cellNorm,cellData: no visible global function definition for
  ‘capture.output’
show,cellData: no visible global function definition for ‘str’
show,expData: no visible global function definition for ‘str’
Undefined global functions or variables:
  abline boxplot capture.output combn read.csv read.delim str strheight
  strwidth write.table
Consider adding
  importFrom("graphics", "abline", "boxplot", "strheight", "strwidth")
  importFrom("utils", "capture.output", "combn", "read.csv",
             "read.delim", "str", "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 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
operaMate 48.289   1.32  63.657
cellViz   13.939   0.43  15.194
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/OperaMate.Rcheck/00check.log’
for details.


OperaMate.Rcheck/00install.out:

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

OperaMate.Rcheck/OperaMate-Ex.timings:

nameusersystemelapsed
cellData-class0.0030.0000.003
cellLoad0.5100.0110.531
cellMean0.0190.0010.020
cellNorm0.0530.0010.054
cellNumLoad0.0080.0010.009
cellQC0.3180.0140.346
cellSig0.9300.0170.972
cellSigAnalysis0.2480.0083.311
cellSigAnalysisPlot1.1080.0154.265
cellSigPlot0.8090.0120.846
cellViz13.939 0.43015.194
data0.0130.0020.015
expData-class0.0060.0000.006
generateReport0.0310.0020.032
loadAll0.4640.0030.490
operaMate48.289 1.32063.657
parseTemplete0.0240.0000.024