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BioC 3.4: CHECK report for GenoGAM on morelia

This page was generated on 2016-09-21 03:55:49 -0700 (Wed, 21 Sep 2016).

Package 487/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 1.1.4
Georg Stricker
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenoGAM
Last Changed Rev: 120049 / Revision: 121152
Last Changed Date: 2016-08-11 01:25:14 -0700 (Thu, 11 Aug 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: GenoGAM
Version: 1.1.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.1.4.tar.gz
StartedAt: 2016-09-20 07:03:16 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:06:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 175.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GenoGAM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenoGAM.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 ‘GenoGAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenoGAM’ version ‘1.1.4’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenoGAM’ 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
.doCrossValidation: no visible global function definition for ‘optim’
.extractSplines: no visible global function definition for
  ‘coefficients’
.getFunctions: no visible global function definition for ‘coefficients’
.loglik : <anonymous>: no visible global function definition for
  ‘dnbinom’
.pvals: no visible global function definition for ‘pnorm’
.updateFormula: no visible global function definition for ‘as.formula’
computeRegionSignificance: no visible global function definition for
  ‘p.adjust’
computeRegionSignificance: no visible binding for global variable
  ‘pvalue’
computeRegionSignificance: no visible binding for global variable
  ‘gene’
genogam: no visible global function definition for ‘as.formula’
makeTestGenoGAM: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula coefficients dnbinom gene optim p.adjust pnorm pvalue
  runif
Consider adding
  importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim",
             "p.adjust", "pnorm", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.


GenoGAM.Rcheck/00install.out:

* installing *source* package ‘GenoGAM’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenoGAM)

GenoGAM.Rcheck/GenoGAM-Ex.timings:

nameusersystemelapsed
GenoGAM-view0.2080.0040.211
GenoGAMDataSet000
GenomicTiles-metrics1.5680.0271.594
GenomicTiles-view0.6620.0020.664
GenomicTiles0.2990.0010.299
changeSettings0.2840.0000.285
checkSettings0.1810.0010.182
computeSizeFactors0.3570.0010.358
dataRange0.1890.0000.189
design0.1840.0010.185
fitGenoGAM0.0010.0000.001
getChunkIndex0.2560.0010.257
getCoordinates0.1690.0000.169
getFits0.0150.0010.015
getIndex0.1880.0000.189
getIndexCoordinates0.2290.0000.228
getTile0.4130.0010.414
makeTestGenoGAM0.0230.0000.023
makeTestGenoGAMDataSet0.1510.0000.152
makeTestGenomicTiles0.1660.0000.165
sizeFactors0.1690.0000.170
subset-GenoGAM-method0.0840.0010.084
subset-GenoGAMDataSet-method0.3160.0000.316
subset-GenomicTiles-method0.3300.0010.331
subsetByOverlaps-GenoGAM-ANY-method0.0490.0000.049
subsetByOverlaps-GenoGAMDataSet-GRanges-method0.3600.0010.360
subsetByOverlaps-GenomicTiles-GRanges-method0.2540.0000.255
tileSettings-elements0.1770.0000.177
tileSettings0.1790.0000.179
untile0.2310.0000.232