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CHECK report for TCC on veracruz1

This page was generated on 2018-04-12 13:37:21 -0400 (Thu, 12 Apr 2018).

Package 1386/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.18.0
Jianqiang Sun
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/TCC
Branch: RELEASE_3_6
Last Commit: d13750f
Last Changed Date: 2017-10-30 12:40:07 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.18.0.tar.gz
StartedAt: 2018-04-12 10:11:56 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:21:38 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 581.9 seconds
RetCode: 0
Status:  OK 
CheckDir: TCC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TCC.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 11.875  0.072  12.245
TCC-class          11.032  0.253  11.479
calcAUCValue       10.725  0.062  11.738
calcNormFactors     8.556  0.071   9.253
plotFCPseudocolor   8.237  0.043   8.573
plot.TCC            7.317  0.122   7.657
* 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: OK

Installation output

TCC.Rcheck/00install.out

* installing *source* package ‘TCC’ ...
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (TCC)

Tests output

TCC.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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

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

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

> 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, cbind, colMeans, colSums, colnames, 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: '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 object is masked from 'package:base':

    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] 0.8598469
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] 0.8734719
NA in cutpts forces recomputation using smallest gap
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ samseq - tmm ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ samseq - deseq ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ samseq - deseq2 ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using samseq ...
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
NA in cutpts forces recomputation using smallest gap
[1] 0.8271812
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] 0.7277
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] 0.7830125
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] 0.8018062
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] 0.7875406
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] 0.8155056
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 checkForExperimentalReplicates(object, modelMatrix) :
  same number of samples and coefficients to fit,
  estimating dispersion by treating samples as replicates.
  please read the ?DESeq section on 'Experiments without replicates'.
  in summary: this analysis only potentially useful for data exploration,
  accurate differential expression analysis requires replication
3: In checkForExperimentalReplicates(object, modelMatrix) :
  same number of samples and coefficients to fit,
  estimating dispersion by treating samples as replicates.
  please read the ?DESeq section on 'Experiments without replicates'.
  in summary: this analysis only potentially useful for data exploration,
  accurate differential expression analysis requires replication
4: In checkForExperimentalReplicates(object, modelMatrix) :
  same number of samples and coefficients to fit,
  estimating dispersion by treating samples as replicates.
  please read the ?DESeq section on 'Experiments without replicates'.
  in summary: this analysis only potentially useful for data exploration,
  accurate differential expression analysis requires replication
5: In checkForExperimentalReplicates(object, modelMatrix) :
  same number of samples and coefficients to fit,
  estimating dispersion by treating samples as replicates.
  please read the ?DESeq section on 'Experiments without replicates'.
  in summary: this analysis only potentially useful for data exploration,
  accurate differential expression analysis requires replication
6: 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 39 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 39 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] 0.9104667
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] 0.8982222
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] 0.9163889
NA in cutpts forces recomputation using smallest gap
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ samseq - tmm ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ samseq - deseq ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ samseq - deseq2 ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using samseq ...
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
NA in cutpts forces recomputation using smallest gap
[1] 0.8867833
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] 0.8745556
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] 0.5912875
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] 0.9232125
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] 0.9033875
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] 0.9360625
NA in cutpts forces recomputation using smallest gap
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ samseq - tmm ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq - [ samseq - deseq ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ samseq - deseq2 ] X 1 )
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using samseq ...
TCC::INFO: TCC does not use the normalization factors when 'test.method = "samseq"'.
TCC::INFO: Done.
NA in cutpts forces recomputation using smallest gap
[1] 0.8705156
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] 0.8904062
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] 0.7669656
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] 0.8120906
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] 0.8118031
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] 0.7779531
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] 0.6336421
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] 0.9379033
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] 0.9244676
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] 0.9400005
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] 0.9159638
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 -- Thu Apr 12 10:21:32 2018 
*********************************************** 
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 
309.745   1.551 315.578

Example timings

TCC.Rcheck/TCC-Ex.timings

nameusersystemelapsed
ROKU0.0730.0030.076
TCC-class11.032 0.25311.479
TCC0.0080.0020.010
WAD0.2390.0080.257
arab0.0390.0040.043
calcAUCValue10.725 0.06211.738
calcNormFactors8.5560.0719.253
clusterSample0.0920.0060.121
estimateDE1.3060.0101.563
filterLowCountGenes0.0710.0040.086
getNormalizedData0.2790.0040.314
getResult1.7250.0091.948
hypoData3.9430.0184.133
hypoData_mg4.4440.0204.524
hypoData_ts0.0030.0020.004
makeFCMatrix0.0040.0000.004
nakai0.0360.0030.043
plot.TCC7.3170.1227.657
plotFCPseudocolor8.2370.0438.573
simulateReadCounts11.875 0.07212.245