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BioC 3.3: CHECK report for Chicago on moscato2

This page was generated on 2016-10-13 12:54:38 -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: rm -rf Chicago.buildbin-libdir Chicago.Rcheck && mkdir Chicago.buildbin-libdir Chicago.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Chicago.buildbin-libdir Chicago_1.0.4.tar.gz >Chicago.Rcheck\00install.out 2>&1 && cp Chicago.Rcheck\00install.out Chicago-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Chicago.buildbin-libdir --install="check:Chicago-install.out" --force-multiarch --no-vignettes --timings Chicago_1.0.4.tar.gz
StartedAt: 2016-10-13 01:56:03 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:59:53 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 230.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Chicago.buildbin-libdir Chicago.Rcheck && mkdir Chicago.buildbin-libdir Chicago.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Chicago.buildbin-libdir Chicago_1.0.4.tar.gz >Chicago.Rcheck\00install.out 2>&1 && cp Chicago.Rcheck\00install.out Chicago-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Chicago.buildbin-libdir --install="check:Chicago-install.out" --force-multiarch --no-vignettes --timings Chicago_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/Chicago.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 12.59   1.17   21.06
exportResults      11.03   0.16   14.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 12.04   1.18   13.85
exportResults      12.23   0.12   13.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/Chicago.Rcheck/00check.log'
for details.


Chicago.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'Chicago' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Chicago' as Chicago_1.0.4.zip
* DONE (Chicago)

Chicago.Rcheck/examples_i386/Chicago-Ex.timings:

nameusersystemelapsed
cdUnitTest0.070.010.08
chicagoData000
chicagoPipeline0.110.000.11
copyCD0.010.000.02
defaultSettings000
estimateBrownianComponent0.580.020.59
estimateDistFun0.040.000.03
estimateTechnicalNoise0.060.000.07
exportResults11.03 0.1614.10
getPvals0.110.010.12
getScores0.040.020.19
getSkOnly0.110.000.11
mergeSamples0.130.000.13
modifySettings0.010.000.01
normaliseBaits0.080.010.09
normaliseOtherEnds12.59 1.1721.06
overlapFragWithFeatures0.120.000.13
peakEnrichment4Features2.280.162.43
plotBaits0.480.010.50
plotDistFun0.050.000.04
readAndMerge0.220.000.22
readSample0.110.000.11
setExperiment0.010.000.02

Chicago.Rcheck/examples_x64/Chicago-Ex.timings:

nameusersystemelapsed
cdUnitTest0.080.010.09
chicagoData000
chicagoPipeline0.120.000.13
copyCD000
defaultSettings000
estimateBrownianComponent0.490.000.48
estimateDistFun0.030.000.03
estimateTechnicalNoise0.060.020.08
exportResults12.23 0.1213.23
getPvals0.120.000.12
getScores0.140.000.14
getSkOnly0.70.00.7
mergeSamples0.120.000.12
modifySettings0.000.020.02
normaliseBaits0.100.020.11
normaliseOtherEnds12.04 1.1813.85
overlapFragWithFeatures0.090.000.09
peakEnrichment4Features2.510.202.71
plotBaits0.30.00.3
plotDistFun0.000.020.06
readAndMerge0.120.000.13
readSample0.080.000.08
setExperiment0.020.000.01