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CHECK report for TCC on merida1

This page was generated on 2021-05-06 12:37:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the TCC package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1841/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.30.0  (landing page)
Jianqiang Sun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/TCC
Branch: RELEASE_3_12
Last Commit: 40c62a0
Last Changed Date: 2020-10-27 10:52:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCC_1.30.0.tar.gz
StartedAt: 2021-05-06 06:47:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:55:29 -0400 (Thu, 06 May 2021)
EllapsedTime: 459.0 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 --install=check:TCC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCC_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TCC.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.30.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
simulateReadCounts 11.363  0.041  11.418
TCC-class           8.592  0.270   8.874
plot.TCC            7.396  0.112   7.519
plotFCPseudocolor   7.298  0.034   7.340
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TCC’ ...
** using staged installation
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TCC)

Tests output

TCC.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'limma'

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

    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 : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7973438
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 : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.8962219
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9030625
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 : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8621406
TCC::INFO: Generating simulation data under NB distribution ...
TCC::INFO: (genesizes   :  1000 )
TCC::INFO: (replicates  :  1, 1 )
TCC::INFO: (PDEG        :  0.16, 0.04 )
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : tmm - [ bayseq - tmm ] X 1 )
TCC::INFO: Done.
TCC::INFO: Calculating normalization factors using DEGES
TCC::INFO: (iDEGES pipeline : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7166687
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 : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.7700469
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 : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7456333
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 : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.9168667
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 : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9319889
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 : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.9075444
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 : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.6236875
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 : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.8667125
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 : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9099937
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 : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8343
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 : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.7021375
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 : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.7795344
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 : deseq2 - [ bayseq - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using bayseq ...
TCC::INFO: Done.
[1] 0.6407402
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 : deseq2 - [ deseq2 - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using deseq2 ...
TCC::INFO: Done.
[1] 0.9093381
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 : deseq2 - [ edger - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using edger ...
TCC::INFO: Done.
[1] 0.9287081
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 : deseq2 - [ voom - deseq2 ] X 1 )
TCC::INFO: Done.
TCC::INFO: Identifying DE genes using voom ...
TCC::INFO: Done.
[1] 0.8946465
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 May  6 06:55:20 2021 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
185.634   1.626 187.601 

Example timings

TCC.Rcheck/TCC-Ex.timings

nameusersystemelapsed
ROKU0.0150.0020.018
TCC-class8.5920.2708.874
TCC0.0090.0030.011
WAD0.2200.0050.225
arab0.0460.0040.051
calcAUCValue3.7650.0333.803
calcNormFactors1.3510.0231.376
clusterSample0.2670.0100.279
estimateDE0.4670.0170.484
filterLowCountGenes0.0210.0040.024
getNormalizedData0.2910.0110.303
getResult0.5270.0100.537
hypoData3.2590.0113.274
hypoData_mg3.7660.0223.791
hypoData_ts0.0020.0030.004
makeFCMatrix0.0040.0010.004
nakai0.0430.0030.047
plot.TCC7.3960.1127.519
plotFCPseudocolor7.2980.0347.340
simulateReadCounts11.363 0.04111.418