Package: XBSeq

Version: 1.14.1

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_1.14.1.tar.gz

StartedAt: 2019-04-16 03:23:22 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:35:08 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 706.2 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_1.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/XBSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.1’
* 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    73.092 22.956  96.126
XBSeq     65.018 20.776  85.790
XBSeqTest 61.757 19.463  81.216
* 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-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
152.001  29.574 181.555 

name	user	system	elapsed
MAplot	73.092	22.956	96.126
XBSeq	65.018	20.776	85.790
XBSeqDataSet-class	0.199	0.018	0.216
XBSeqTest	61.757	19.463	81.216
XBplot	0.432	0.033	0.465
conditions	0.145	0.012	0.157
counts	0.147	0.013	0.160
dispEst	3.410	0.759	4.169
dispTable	2.956	0.753	3.709
estimateRealCount	0.166	0.016	0.182
estimateSCV	2.994	0.742	3.734
fitInfo	3.504	0.786	4.290
getSignalVars	2.334	0.699	3.033
plotSCVEsts	3.144	0.802	3.946