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BioC 3.3: CHECK report for Chicago on zin2

This page was generated on 2016-10-13 12:46:11 -0700 (Thu, 13 Oct 2016).

Package 173/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.0.4
Mikhail Spivakov
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Chicago
Last Changed Rev: 121590 / Revision: 122332
Last Changed Date: 2016-09-30 07:58:25 -0700 (Fri, 30 Sep 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Chicago
Version: 1.0.4
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.0.4.tar.gz
StartedAt: 2016-10-13 00:18:49 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 00:20:19 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 89.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Chicago.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 ‘Chicago/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Chicago’ version ‘1.0.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Chicago’ 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 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
.addTLB: no visible global function definition for ‘quantile’
.binning: no visible binding for global variable ‘dist’
.estimateDispersion: no visible binding for global variable ‘dist’
.getAvgFragLength: no visible binding for global variable ‘end’
.getNoOfHypotheses: no visible binding for global variable ‘end’
.getSampleScalingFactors: no visible global function definition for
  ‘median’
.getWeights: no visible binding for global variable ‘end’
.normaliseFragmentSets: no visible global function definition for
  ‘median’
.normaliseFragmentSets: no visible global function definition for
  ‘predict’
.normaliseFragmentSets: no visible global function definition for
  ‘loess’
.normaliseFragmentSets: no visible global function definition for ‘pdf’
.normaliseFragmentSets: no visible global function definition for ‘par’
.normaliseFragmentSets: no visible global function definition for
  ‘lines’
.normaliseFragmentSets: no visible global function definition for
  ‘dev.off’
.normaliseFragmentSets: no visible global function definition for
  ‘pgamma’
.plotNumberOL: no visible binding for global variable ‘dist’
.plotNumberOL: no visible binding for global variable ‘sd’
.plotNumberOL: no visible global function definition for ‘pdf’
.plotNumberOL: no visible global function definition for ‘barplot’
.plotNumberOL: no visible global function definition for ‘arrows’
.plotNumberOL: no visible global function definition for ‘dev.off’
.splitCHiC: no visible global function definition for ‘read.table’
.splitCHiC: no visible binding for global variable ‘dist’
estimateDistFun: no visible global function definition for ‘lm’
estimateDistFun: no visible global function definition for ‘pdf’
estimateDistFun: no visible global function definition for ‘legend’
estimateDistFun: no visible global function definition for ‘dev.off’
estimateTechnicalNoise: no visible global function definition for ‘pdf’
estimateTechnicalNoise: no visible global function definition for ‘par’
estimateTechnicalNoise: no visible global function definition for
  ‘boxplot’
estimateTechnicalNoise: no visible global function definition for
  ‘dev.off’
exportResults: no visible global function definition for ‘write.table’
getPvals: no visible global function definition for ‘ppois’
getPvals: no visible global function definition for ‘pnbinom’
normaliseOtherEnds: no visible global function definition for ‘pdf’
normaliseOtherEnds: no visible global function definition for ‘legend’
normaliseOtherEnds: no visible global function definition for ‘dev.off’
peakEnrichment4Features: no visible global function definition for
  ‘plot’
peakEnrichment4Features: no visible global function definition for
  ‘density’
peakEnrichment4Features: no visible global function definition for
  ‘lines’
plotBaits: no visible global function definition for ‘pdf’
plotBaits: no visible global function definition for ‘par’
plotBaits: no visible global function definition for ‘plot’
plotBaits: no visible global function definition for ‘abline’
plotBaits: no visible global function definition for ‘lines’
plotBaits: no visible global function definition for ‘dev.off’
plotDistFun: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline arrows barplot boxplot density dev.off dist end legend lines
  lm loess median par pdf pgamma plot pnbinom ppois predict quantile
  read.table sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "arrows", "barplot", "boxplot",
             "legend", "lines", "par", "plot")
  importFrom("stats", "density", "dist", "end", "lm", "loess", "median",
             "pgamma", "pnbinom", "ppois", "predict", "quantile", "sd")
  importFrom("utils", "read.table", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 9.895  1.891  12.527
exportResults      8.862  0.246   9.601
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/Chicago.Rcheck/00check.log’
for details.


Chicago.Rcheck/00install.out:

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

Chicago.Rcheck/Chicago-Ex.timings:

nameusersystemelapsed
cdUnitTest0.0520.0010.062
chicagoData0.0010.0000.001
chicagoPipeline0.0700.0000.071
copyCD0.0080.0000.007
defaultSettings0.0000.0000.001
estimateBrownianComponent0.3500.0000.351
estimateDistFun0.0280.0000.029
estimateTechnicalNoise0.1490.0000.149
exportResults8.8620.2469.601
getPvals0.1220.0000.121
getScores0.0680.0000.068
getSkOnly0.0930.0080.102
mergeSamples0.1270.0000.127
modifySettings0.0130.0000.016
normaliseBaits0.0830.0000.085
normaliseOtherEnds 9.895 1.89112.527
overlapFragWithFeatures0.0730.0000.073
peakEnrichment4Features1.9850.0372.086
plotBaits0.2690.0000.271
plotDistFun0.0130.0000.012
readAndMerge0.0980.0000.105
readSample0.0620.0030.069
setExperiment0.0090.0000.009