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BioC 3.4: CHECK report for BiSeq on morelia

This page was generated on 2017-04-15 16:24:42 -0400 (Sat, 15 Apr 2017).

Package 135/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiSeq 1.14.0
Katja Hebestreit
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BiSeq
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiSeq
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.14.0.tar.gz
StartedAt: 2017-04-14 23:18:14 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:23:05 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 290.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BiSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.14.0’
* 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 ... 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 ‘BiSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Formula’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Formula’
  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
.betaRegression : inv.link: no visible global function definition for
  ‘pnorm’
.betaRegression : beta.regr: no visible global function definition for
  ‘as.formula’
.categorialColors: no visible global function definition for ‘colors’
.estLocCor: no visible global function definition for ‘combn’
.logisticRegression : inv.link: no visible global function definition
  for ‘pnorm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘lm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘as.formula’
.makeVariogram: no visible global function definition for ‘qnorm’
.plotBindingSites: no visible global function definition for
  ‘txtProgressBar’
.plotBindingSites: no visible global function definition for
  ‘setTxtProgressBar’
.plotBindingSites : <anonymous>: no visible global function definition
  for ‘ksmooth’
.plotBindingSites: no visible global function definition for ‘rainbow’
.plotBindingSites: no visible binding for global variable ‘plot’
.plotBindingSites: no visible global function definition for ‘lines’
.plotBindingSites: no visible global function definition for ‘rgb’
.plotBindingSites: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘rgb’
.plotMeth: no visible binding for global variable ‘plot’
.plotMeth: no visible global function definition for ‘lines’
.plotMeth: no visible global function definition for ‘legend’
.plotMethMap: no visible global function definition for
  ‘colorRampPalette’
.plotMethMap: no visible binding for global variable ‘heatmap’
.plotSmoothMeth: no visible global function definition for ‘rainbow’
.plotSmoothMeth: no visible binding for global variable ‘plot’
.plotSmoothMeth: no visible global function definition for ‘lines’
.predictMeth: no visible global function definition for
  ‘txtProgressBar’
.predictMeth: no visible global function definition for
  ‘setTxtProgressBar’
.testClusters: no visible global function definition for ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘qnorm’
.trimClusters : integrand: no visible global function definition for
  ‘dnorm’
.trimClusters: no visible global function definition for ‘integrate’
.trimClusters: no visible global function definition for ‘pnorm’
.trimClusters: no visible global function definition for ‘qnorm’
.variogram: no visible global function definition for ‘dist’
.variogram: no visible global function definition for ‘txtProgressBar’
.variogram: no visible global function definition for
  ‘setTxtProgressBar’
.writeBED_BSraw: no visible global function definition for ‘colorRamp’
.writeBED_BSraw: no visible global function definition for ‘rgb’
.writeBED_BSrel: no visible global function definition for ‘colorRamp’
.writeBED_BSrel: no visible global function definition for ‘rgb’
betaRegression,formula-character-BSrel-numeric : inv.link: no visible
  global function definition for ‘pnorm’
betaRegression,formula-character-BSrel-numeric : beta.regr: no visible
  global function definition for ‘as.formula’
estLocCor,list: no visible global function definition for ‘combn’
logisticRegression,formula-character-BSrel-numeric : inv.link: no
  visible global function definition for ‘pnorm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘lm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘as.formula’
makeVariogram,data.frame-logical-numeric-numeric: no visible global
  function definition for ‘qnorm’
plotMethMap,BSrel-GRanges-factor-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-logical: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-factor-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-missing: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-logical: no visible binding for
  global variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-missing: no visible binding for
  global variable ‘heatmap’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘txtProgressBar’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘setTxtProgressBar’
testClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘qnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘dnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘integrate’
trimClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘qnorm’
writeBED,BSraw-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSraw-character-character: no visible global function
  definition for ‘rgb’
writeBED,BSrel-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSrel-character-character: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  as.formula col2rgb colorRamp colorRampPalette colors combn dist dnorm
  heatmap integrate ksmooth legend lines lm plot pnorm qnorm rainbow
  rgb setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "colorRampPalette",
             "colors", "rainbow", "rgb")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "dist", "dnorm", "heatmap",
             "integrate", "ksmooth", "lm", "pnorm", "qnorm")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
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
globalTest     21.728  0.052  21.787
betaRegression 16.675  0.681  17.489
makeVariogram   6.361  0.672   7.062
estLocCor       6.144  0.580   6.763
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/BiSeq.Rcheck/00check.log’
for details.


BiSeq.Rcheck/00install.out:

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

BiSeq.Rcheck/BiSeq-Ex.timings:

nameusersystemelapsed
BSraw-class0.1900.0070.198
BSrel-class0.1010.0050.106
DMRs0.0400.0020.041
annotateGRanges0.1980.0080.206
betaRegression16.675 0.68117.489
betaResults0.0070.0010.007
betaResultsNull0.0040.0000.005
binomLikelihoodSmooth0.0050.0000.006
clusterSites0.3410.1690.552
clusterSitesToGR0.3970.1970.570
compareTwoSamples2.6121.7094.148
covBoxplots0.1040.0150.119
covStatistics0.0650.0110.076
estLocCor6.1440.5806.763
filterByCov0.2440.0270.271
filterBySharedRegions0.1060.0100.115
findDMRs0.7440.0170.763
globalTest21.728 0.05221.787
limitCov0.5400.3111.226
logisticRegression1.7190.0581.778
makeVariogram6.3610.6727.062
plotBindingSites1.9820.0592.045
plotMeth0.1940.0110.206
plotMethMap0.2140.0120.225
plotSmoothMeth0.1150.0090.125
predictMeth1.1330.7481.470
predictedMeth0.0180.0090.027
promoters0.0620.0120.074
rawToRel0.0580.0130.071
readBismark0.0670.0080.075
rrbs0.0440.0100.054
smoothVariogram0.0240.0030.032
summarizeRegions1.2380.4091.706
testClusters0.0770.0040.081
trimClusters0.5860.0360.622
vario0.0020.0000.003
writeBED0.2010.0140.216