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BioC 3.4: CHECK report for OperaMate on zin1

This page was generated on 2016-09-21 03:39:57 -0700 (Wed, 21 Sep 2016).

Package 848/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OperaMate 1.5.0
Chenglin Liu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OperaMate
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 ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OperaMate
Version: 1.5.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OperaMate_1.5.0.tar.gz
StartedAt: 2016-09-20 10:10:44 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:12:18 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 93.6 seconds
RetCode: 0
Status:  OK 
CheckDir: OperaMate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OperaMate_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/OperaMate.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 ‘OperaMate/DESCRIPTION’ ... OK
* this is package ‘OperaMate’ version ‘1.5.0’
* 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 33.272  0.020  41.097
cellViz    9.448  0.012   9.462
* 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
  ‘/home/biocbuild/bbs-3.4-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-class0.0000.0000.003
cellLoad0.4240.0040.427
cellMean0.0080.0000.010
cellNorm0.0360.0000.038
cellNumLoad0.0080.0000.008
cellQC0.2160.0040.220
cellSig0.6560.0120.670
cellSigAnalysis0.1320.0083.597
cellSigAnalysisPlot0.1720.0002.189
cellSigPlot0.2160.0000.214
cellViz9.4480.0129.462
data0.0080.0000.011
expData-class0.0000.0000.002
generateReport0.0200.0000.018
loadAll0.4200.0000.419
operaMate33.272 0.02041.097
parseTemplete0.0240.0000.026