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BioC 3.5: CHECK report for XBSeq on toluca2

This page was generated on 2017-04-23 14:40:14 -0400 (Sun, 23 Apr 2017).

Package 1367/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XBSeq 1.5.2
Yuanhang Liu
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/XBSeq
Last Changed Rev: 125170 / Revision: 129046
Last Changed Date: 2016-12-14 18:05:29 -0500 (Wed, 14 Dec 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: XBSeq
Version: 1.5.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XBSeq_1.5.2.tar.gz
StartedAt: 2017-04-23 11:14:01 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 11:27:17 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 796.6 seconds
RetCode: 0
Status:  OK 
CheckDir: XBSeq.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 XBSeq_1.5.2.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/XBSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XBSeq’ version ‘1.5.2’
* 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 ‘XBSeq’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘XBSeq’ for: ‘conditions’, ‘conditions<-’, ‘dispTable’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Loglikhood : <anonymous>: no visible global function definition for
  ‘ddelap’
Loglikhood : <anonymous>: no visible global function definition for
  ‘dpois’
Loglikhood_NB : <anonymous>: no visible global function definition for
  ‘dnbinom’
MAplot: no visible binding for global variable ‘baseMean’
MAplot: no visible global function definition for ‘quantile’
MAplot: no visible binding for global variable ‘log2FoldChange’
XBSeqDataSet: no visible global function definition for ‘DataFrame’
XBSeqDataSet: no visible global function definition for
  ‘SummarizedExperiment’
XBSeqDataSet: no visible global function definition for ‘formula’
XBSeqTest: no visible global function definition for ‘dispTable’
XBSeqTest: no visible global function definition for ‘conditions’
XBSeqTest: no visible global function definition for ‘p.adjust’
XBSeqTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
XBplot: no visible global function definition for ‘median’
XBplot: no visible binding for global variable ‘Sample’
XBplot: no visible binding for global variable ‘Group’
XBplot: no visible binding for global variable ‘..count..’
adjustScv: no visible global function definition for ‘data’
adjustScv: no visible binding for global variable
  ‘scvBiasCorrectionFits’
estimation_param_PoissonNB_MLE: no visible global function definition
  for ‘optim’
estimation_param_PoissonNB_MLE_NB: no visible global function
  definition for ‘optim’
exactTestBetaApprox: no visible global function definition for ‘qbeta’
exactTestBetaApprox: no visible global function definition for ‘pbeta’
getSignalVars: no visible global function definition for ‘cor’
parametricscvFit: no visible global function definition for ‘glm’
parametricscvFit: no visible global function definition for ‘Gamma’
parametricscvFit: no visible global function definition for
  ‘coefficients’
plotSCVEsts: no visible global function definition for ‘complete.cases’
predict_helper: no visible global function definition for ‘predict’
prepareScvBiasCorrectionFits : <anonymous> : <anonymous>: no visible
  global function definition for ‘rnbinom’
counts,XBSeqDataSet: no visible global function definition for ‘assays’
counts,XBSeqDataSet: no visible global function definition for ‘assay’
estimateRealCount,XBSeqDataSet: no visible global function definition
  for ‘assay’
estimateRealCount,XBSeqDataSet: no visible global function definition
  for ‘assay<-’
estimateSCV,XBSeqDataSet: no visible global function definition for
  ‘conditions’
estimateSCV,XBSeqDataSet: no visible global function definition for
  ‘dispTable<-’
Undefined global functions or variables:
  ..count.. DataFrame Gamma Group Sample SummarizedExperiment assay
  assay<- assays baseMean coefficients complete.cases conditions cor
  data ddelap dispTable dispTable<- dnbinom dpois formula glm
  log2FoldChange median optim p.adjust pbeta predict qbeta quantile
  rnbinom scvBiasCorrectionFits
Consider adding
  importFrom("stats", "Gamma", "coefficients", "complete.cases", "cor",
             "dnbinom", "dpois", "formula", "glm", "median", "optim",
             "p.adjust", "pbeta", "predict", "qbeta", "quantile",
             "rnbinom")
  importFrom("utils", "data")
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
MAplot    101.941 12.159 115.696
XBSeq      97.147 13.286 110.710
XBSeqTest  83.226 13.031  96.292
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/XBSeq.Rcheck/00check.log’
for details.


XBSeq.Rcheck/00install.out:

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

XBSeq.Rcheck/XBSeq-Ex.timings:

nameusersystemelapsed
MAplot101.941 12.159115.696
XBSeq 97.147 13.286110.710
XBSeqDataSet-class0.1840.0140.198
XBSeqTest83.22613.03196.292
XBplot1.2650.0371.305
conditions0.1230.0150.138
counts0.1260.0120.138
dispEst3.0830.7453.828
dispTable3.1760.6923.871
estimateRealCount0.1150.0130.129
estimateSCV2.4750.6703.145
fitInfo2.8380.6953.533
getSignalVars2.7610.6893.452
plotSCVEsts2.8480.7663.616