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BioC 3.4: CHECK report for XBSeq on malbec1

This page was generated on 2017-04-15 16:13:05 -0400 (Sat, 15 Apr 2017).

Package 1286/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XBSeq 1.4.0
Yuanhang Liu
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/XBSeq
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  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: XBSeq
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings XBSeq_1.4.0.tar.gz
StartedAt: 2017-04-15 01:52:41 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 02:01:36 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 535.1 seconds
RetCode: 0
Status:  OK 
CheckDir: XBSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings XBSeq_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/XBSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 ‘XBSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
  ‘dpois’
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 binding for global
  variable ‘bgcounts’
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’
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 bgcounts coefficients complete.cases
  conditions cor data 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    90.408  0.020  90.533
XBSeq     88.520  0.036  88.639
XBSeqTest 71.964  0.024  72.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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
MAplot90.408 0.02090.533
XBSeq88.520 0.03688.639
XBSeqDataSet-class0.1400.0040.144
XBSeqTest71.964 0.02472.032
XBplot0.3520.0040.357
conditions0.0920.0040.093
counts0.0920.0000.095
dispEst2.4480.0082.458
dispTable2.5000.0042.508
estimateRealCount0.1160.0000.113
estimateSCV2.5960.0002.598
fitInfo2.3240.0042.328
getSignalVars2.0040.0042.010
plotSCVEsts2.5800.0122.593