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BioC 3.3: CHECK report for epigenomix on oaxaca

This page was generated on 2016-10-13 12:58:59 -0700 (Thu, 13 Oct 2016).

Package 356/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.12.0
Hans-Ulrich Klein
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/epigenomix
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: epigenomix
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.12.0.tar.gz
StartedAt: 2016-10-13 01:17:53 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:22:21 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 268.5 seconds
RetCode: 0
Status:  OK 
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/epigenomix.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.12.0’
* 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 ‘epigenomix’ 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
.bayesMixModel: no visible global function definition for ‘rgamma’
.bayesMixModel: no visible global function definition for ‘dnorm’
.bayesMixModel: no visible global function definition for ‘dexp’
.bayesMixModel: no visible global function definition for ‘dgamma’
.bayesMixModel: no visible binding for global variable ‘dnorm’
.bayesMixModel : <anonymous>: no visible global function definition for
  ‘dexp’
.bayesMixModel: no visible binding for global variable ‘dexp’
.bayesMixModel : <anonymous>: no visible global function definition for
  ‘dgamma’
.bayesMixModel: no visible binding for global variable ‘dgamma’
.mlMixModel: no visible binding for global variable ‘dnorm’
.mlMixModel : <anonymous>: no visible global function definition for
  ‘dexp’
.mlMixModel: no visible binding for global variable ‘dexp’
.mlMixModel: no visible global function definition for ‘dnorm’
.mlMixModel: no visible global function definition for ‘dexp’
.plotChains: no visible global function definition for ‘par’
.plotChains: no visible binding for global variable ‘plot’
.plotClassification: no visible binding for global variable ‘plot’
.plotClassification: no visible global function definition for ‘points’
.plotComponents: no visible binding for global variable ‘plot’
.plotComponents: no visible binding for global variable ‘hist’
.plotComponents: no visible global function definition for ‘lines’
.sampleAllocations: no visible global function definition for ‘dnorm’
.sampleAllocations: no visible global function definition for ‘dexp’
.sampleAllocations: no visible global function definition for ‘dgamma’
.sampleAllocations: no visible global function definition for ‘runif’
.sampleAlpha: no visible global function definition for ‘rnorm’
.sampleAlpha: no visible global function definition for ‘dnorm’
.sampleAlpha: no visible global function definition for ‘dgamma’
.sampleAlpha: no visible global function definition for ‘runif’
.sampleComponentParameters: no visible global function definition for
  ‘rgamma’
.sampleMixtureTDP: no visible global function definition for ‘rbeta’
.sampleShape: no visible global function definition for ‘dgamma’
.sampleShape: no visible global function definition for ‘rnorm’
.sampleShape: no visible global function definition for ‘dnorm’
.sampleShape: no visible global function definition for ‘runif’
bayesMixModel,numeric: no visible global function definition for
  ‘rgamma’
bayesMixModel,numeric: no visible global function definition for
  ‘dnorm’
bayesMixModel,numeric: no visible global function definition for ‘dexp’
bayesMixModel,numeric: no visible global function definition for
  ‘dgamma’
bayesMixModel,numeric: no visible binding for global variable ‘dnorm’
bayesMixModel,numeric : <anonymous>: no visible global function
  definition for ‘dexp’
bayesMixModel,numeric: no visible binding for global variable ‘dexp’
bayesMixModel,numeric : <anonymous>: no visible global function
  definition for ‘dgamma’
bayesMixModel,numeric: no visible binding for global variable ‘dgamma’
mlMixModel,numeric: no visible binding for global variable ‘dnorm’
mlMixModel,numeric : <anonymous>: no visible global function definition
  for ‘dexp’
mlMixModel,numeric: no visible binding for global variable ‘dexp’
mlMixModel,numeric: no visible global function definition for ‘dnorm’
mlMixModel,numeric: no visible global function definition for ‘dexp’
plotChains,MixModelBayes: no visible global function definition for
  ‘par’
plotChains,MixModelBayes: no visible binding for global variable ‘plot’
plotClassification,MixModel: no visible binding for global variable
  ‘plot’
plotClassification,MixModel: no visible global function definition for
  ‘points’
plotComponents,MixModel: no visible binding for global variable ‘plot’
plotComponents,MixModel: no visible binding for global variable ‘hist’
plotComponents,MixModel: no visible global function definition for
  ‘lines’
Undefined global functions or variables:
  dexp dgamma dnorm hist lines par plot points rbeta rgamma rnorm runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot", "points")
  importFrom("stats", "dexp", "dgamma", "dnorm", "rbeta", "rgamma",
             "rnorm", "runif")
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
plotChains    34.208  0.086  34.340
bayesMixModel 26.414  0.146  27.289
mlMixModel    15.320  0.055  15.508
* 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-3.3-bioc/meat/epigenomix.Rcheck/00check.log’
for details.


epigenomix.Rcheck/00install.out:

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

epigenomix.Rcheck/epigenomix-Ex.timings:

nameusersystemelapsed
ChIPseqSet-class0.0030.0000.002
MixModel-class0.0010.0000.001
MixModelBayes-class0.0010.0000.001
MixModelML-class0.0010.0000.001
MixtureComponent-class0.0000.0000.001
bayesMixModel26.414 0.14627.289
calculateCrossCorrelation0.6600.0040.665
eSet0.0180.0010.020
fpkm0.0370.0030.039
getAlignmentQuality0.0010.0000.000
integrateData0.1710.0000.171
mappedReads0.0390.0020.041
matchProbeToPromoter0.2580.0010.260
mlMixModel15.320 0.05515.508
normalize0.0460.0000.047
normalizeChIP0.0420.0010.043
plotChains34.208 0.08634.340
plotClassification0.0310.0010.032
plotComponents0.0390.0000.041
summarizeReads0.1790.0000.179
transToTSS0.0030.0010.004