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CHECK report for TCC on malbec2

This page was generated on 2020-10-17 11:55:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TCC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1783/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.28.0
Jianqiang Sun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TCC
Branch: RELEASE_3_11
Last Commit: 61930ac
Last Changed Date: 2020-04-27 14:36:08 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.28.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TCC_1.28.0.tar.gz
StartedAt: 2020-10-17 05:59:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:09:36 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 596.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: TCC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TCC_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TCC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.28.0’
* 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 ‘TCC’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/TCC.Rcheck/00install.out’ for details.
* 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 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
TCC-class          9.349  0.124   9.473
calcNormFactors    8.237  0.008   8.252
calcAUCValue       7.683  0.008   7.691
simulateReadCounts 6.754  0.004   6.758
plot.TCC           6.430  0.028   6.460
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/TCC.Rcheck/00check.log’
for details.

Installation output

TCC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TCC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘TCC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
Creating a new generic function for ‘calcNormFactors’ in package ‘TCC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package keeps a record of temporary installation path
* DONE (TCC)

Tests output

TCC.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("TCC")

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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, rowsum


Attaching package: 'DESeq2'

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

    estimateSizeFactorsForMatrix, getVarianceStabilizedData,
    varianceStabilizingTransformation


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

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

    plotMA


Attaching package: 'TCC'

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

    calcNormFactors

TCC::INFO: Identifying DE genes using wad ...
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using wad ...
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using tmm ...
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 3 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 2 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 3 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 3 )
TCC::INFO: Done.
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  3, 3 )
TCC::INFO: (PDEG        :  0.16, 0.04 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7532188
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.8952156
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq2 - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.8962219
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9032656
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ voom - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ voom - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8621406
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  1, 1 )
TCC::INFO: (PDEG        :  0.16, 0.04 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.671375
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
3: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
4: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
5: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.7860781
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.7830156
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (samples     :  8 )
TCC::INFO: (factors     :  2 )
TCC::INFO: (PDEG        :  0.1 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7205556
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: There were 45 warnings (use warnings() to see them)
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: There were 45 warnings (use warnings() to see them)
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.9081556
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq2 - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.8777111
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.8991556
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ voom - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ voom - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8684556
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  3, 3, 3 )
TCC::INFO: (PDEG        :  0.12, 0.04, 0.04 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.5969281
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.9094719
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq2 - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.8890813
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9186719
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ voom - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ voom - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8574969
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  1, 1, 1 )
TCC::INFO: (PDEG        :  0.12, 0.04, 0.04 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7142188
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
Error in .local(object, ...) : 
  None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning messages:
1: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
2: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.8001219
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.7622281
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (samples     :  12 )
TCC::INFO: (factors     :  2 )
TCC::INFO: (PDEG        :  0.1 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ bayseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.6314067
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq ...
TCC::INFO: Done.
[1] 0.9402424
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ deseq2 - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.9231656
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ edger - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9418211
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ voom - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ voom - deseq ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.9131522
TCC::INFO: Calculating normalization factors using tmm ...
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using tmm ...
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  3, 3 )
TCC::INFO: (PDEG        :  0.18, 0.02 )
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  3, 3, 3 )
TCC::INFO: (PDEG        :  0.18, 0.01, 0.01 )


RUNIT TEST PROTOCOL -- Sat Oct 17 06:09:31 2020 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TCC RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
341.524   0.641 342.521

Example timings

TCC.Rcheck/TCC-Ex.timings

nameusersystemelapsed
ROKU0.0110.0010.011
TCC-class9.3490.1249.473
TCC0.0090.0030.013
WAD0.2140.0040.218
arab0.0550.0030.059
calcAUCValue7.6830.0087.691
calcNormFactors8.2370.0088.252
clusterSample0.2620.0080.271
estimateDE1.6660.0041.670
filterLowCountGenes0.0310.0000.031
getNormalizedData0.3670.0040.370
getResult2.2060.0002.207
hypoData3.5010.0003.501
hypoData_mg3.6020.0003.602
hypoData_ts0.0020.0000.002
makeFCMatrix0.0030.0000.004
nakai0.0540.0000.053
plot.TCC6.4300.0286.460
plotFCPseudocolor4.7490.0004.765
simulateReadCounts6.7540.0046.758