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CHECK report for TCC on tokay1

This page was generated on 2019-04-13 11:23:09 -0400 (Sat, 13 Apr 2019).

Package 1545/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.22.1
Jianqiang Sun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TCC
Branch: RELEASE_3_8
Last Commit: bb586e8
Last Changed Date: 2019-01-04 13:18:01 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.22.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCC_1.22.1.tar.gz
StartedAt: 2019-04-13 05:52:50 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:12:26 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1176.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TCC.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCC_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCC' version '1.22.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'TCC' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:66: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:73: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:81: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:128: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:152: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/getResult.Rd:20: file link 'plot' in package 'TCC' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
simulateReadCounts 19.86   0.01   20.02
calcAUCValue       17.98   0.03   18.02
TCC-class          15.39   0.14   15.53
calcNormFactors    13.42   0.05   13.46
plotFCPseudocolor  12.70   0.02   12.71
plot.TCC           10.84   0.01   10.93
hypoData            7.17   0.00    7.18
hypoData_mg         6.75   0.01    6.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
simulateReadCounts 21.18   0.03   21.22
calcAUCValue       14.44   0.00   14.44
TCC-class          13.70   0.11   13.81
plotFCPseudocolor  13.35   0.02   13.36
calcNormFactors    11.29   0.00   11.30
plot.TCC            9.72   0.03    9.75
hypoData            6.72   0.00    6.72
hypoData_mg         6.36   0.00    6.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCC.Rcheck/00check.log'
for details.

Installation output

TCC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/TCC_1.22.1.tar.gz && rm -rf TCC.buildbin-libdir && mkdir TCC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCC.buildbin-libdir TCC_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TCC_1.22.1.zip && rm TCC_1.22.1.tar.gz TCC_1.22.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  860k  100  860k    0     0  20.4M      0 --:--:-- --:--:-- --:--:-- 22.7M

install for i386

* installing *source* package 'TCC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'calcNormFactors' in package 'TCC'
** help
*** installing help indices
  converting help for package 'TCC'
    finding HTML links ... done
    ROKU                                    html  
    TCC-class                               html  
    TCC                                     html  
    WAD                                     html  
    arab                                    html  
    calcAUCValue                            html  
    calcNormFactors                         html  
    clusterSample                           html  
    estimateDE                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:66: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:73: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:81: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:128: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/estimateDE.Rd:152: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
    filterLowCountGenes                     html  
    getNormalizedData                       html  
    getResult                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaW0cGj/R.INSTALL1480e6561d5/TCC/man/getResult.Rd:20: file link 'plot' in package 'TCC' does not exist and so has been treated as a topic
    hypoData                                html  
    hypoData_mg                             html  
    hypoData_ts                             html  
    makeFCMatrix                            html  
    nakai                                   html  
    plot.TCC                                html  
    plotFCPseudocolor                       html  
    simulateReadCounts                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TCC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCC' as TCC_1.22.1.zip
* DONE (TCC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TCC' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

TCC.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Welcome to Bioconductor

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

locfit 1.5-9.1 	 2013-03-22
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


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


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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7357281
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8601875
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8598281
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8734625
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8310656
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6686031
NA in cutpts forces recomputation using smallest gap
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).
3: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
4: 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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8193219
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.80945
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6295278
NA in cutpts forces recomputation using smallest gap
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 43 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 43 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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8933889
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8666111
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8878222
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8541889
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6940969
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9056812
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.88775
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9158812
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8508562
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7291594
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8036156
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7655781
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6626682
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9061809
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9016178
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9216906
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8510324
NA in cutpts forces recomputation using smallest gap
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 Apr 13 06:06:45 2019 
*********************************************** 
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 
 334.57    1.06  340.39

TCC.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Welcome to Bioconductor

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

locfit 1.5-9.1 	 2013-03-22
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


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


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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7357281
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8601875
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8598406
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8730375
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8310656
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6686031
NA in cutpts forces recomputation using smallest gap
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).
3: In .local(object, ...) :
  in estimateDispersions: Ignoring extra argument(s).
4: 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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8193219
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8095375
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6295278
NA in cutpts forces recomputation using smallest gap
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 43 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 43 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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8933889
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8666111
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8878222
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8541889
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6940969
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9056812
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.88775
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9158812
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8508562
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7288406
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8036156
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.7655781
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.6626682
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9061809
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9016178
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.9216906
NA in cutpts forces recomputation using smallest gap
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.
NA in cutpts forces recomputation using smallest gap
[1] 0.8510324
NA in cutpts forces recomputation using smallest gap
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 Apr 13 06:12:21 2019 
*********************************************** 
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 
 334.31    0.67  335.32

Example timings

TCC.Rcheck/examples_i386/TCC-Ex.timings

nameusersystemelapsed
ROKU0.030.000.03
TCC-class15.39 0.1415.53
TCC0.020.000.01
WAD0.210.010.24
arab0.080.000.08
calcAUCValue17.98 0.0318.02
calcNormFactors13.42 0.0513.46
clusterSample0.070.000.07
estimateDE1.760.021.78
filterLowCountGenes0.030.010.04
getNormalizedData0.50.00.5
getResult2.460.002.46
hypoData7.170.007.18
hypoData_mg6.750.016.76
hypoData_ts0.000.020.02
makeFCMatrix000
nakai0.050.000.04
plot.TCC10.84 0.0110.93
plotFCPseudocolor12.70 0.0212.71
simulateReadCounts19.86 0.0120.02

TCC.Rcheck/examples_x64/TCC-Ex.timings

nameusersystemelapsed
ROKU0.000.010.01
TCC-class13.70 0.1113.81
TCC0.010.000.01
WAD0.130.000.13
arab0.030.020.04
calcAUCValue14.44 0.0014.44
calcNormFactors11.29 0.0011.30
clusterSample0.060.000.06
estimateDE1.440.001.44
filterLowCountGenes0.030.000.03
getNormalizedData0.320.000.31
getResult1.960.011.99
hypoData6.720.006.72
hypoData_mg6.360.006.36
hypoData_ts000
makeFCMatrix000
nakai0.030.020.04
plot.TCC9.720.039.75
plotFCPseudocolor13.35 0.0213.36
simulateReadCounts21.18 0.0321.22