Package: XBSeq

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XBSeq_1.12.0.tar.gz

StartedAt: 2018-10-17 00:39:27 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:51:12 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 704.9 seconds

RetCode: 0

Status:  OK

CheckDir: XBSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XBSeq_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/XBSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 ‘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 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    69.696 22.972  92.713
XBSeq     65.870 19.816  85.682
XBSeqTest 61.910 19.583  81.489
* 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-3.7-bioc/meat/XBSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL XBSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘XBSeq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘XBSeq.Rmd’ using ‘UTF-8’ 
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
** testing if installed package can be loaded
* DONE (XBSeq)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(XBSeq)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

    Welcome to 'XBSeq'.
> 
> test_check("XBSeq")
estimating parameters using MLE for group one 
estimating parameters using MLE for group two 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
149.699  32.902 182.578 

name	user	system	elapsed
MAplot	69.696	22.972	92.713
XBSeq	65.870	19.816	85.682
XBSeqDataSet-class	0.190	0.019	0.209
XBSeqTest	61.910	19.583	81.489
XBplot	0.432	0.031	0.464
conditions	0.143	0.016	0.160
counts	0.137	0.010	0.147
dispEst	3.294	0.714	4.009
dispTable	2.886	0.725	3.611
estimateRealCount	0.157	0.015	0.171
estimateSCV	2.941	0.722	3.663
fitInfo	3.342	0.734	4.076
getSignalVars	2.388	0.722	3.110
plotSCVEsts	3.211	0.767	3.981