Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-06 11:06:48 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TCC on nebbiolo1


To the developers/maintainers of the TCC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2004/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.39.0  (landing page)
Jianqiang Sun
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/TCC
git_branch: master
git_last_commit: d0e3c35
git_last_commit_date: 2022-11-01 11:08:38 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'baySeq' which is not available
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available

Summary

Package: TCC
Version: 1.39.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TCC_1.39.0.tar.gz
StartedAt: 2022-12-05 23:53:06 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-06 00:01:25 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 499.2 seconds
RetCode: 0
Status:   OK  
CheckDir: TCC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TCC_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TCC.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.39.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
TCC-class 6.372  0.231   6.605
* 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 ...
  ‘TCC.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

TCC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TCC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> BiocGenerics:::testPackage("TCC")

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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 objects are masked from 'package:base':

    I, expand.grid, unname


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] 0.8923281
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: (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] 0.7946778
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] 0.8696778
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] 0.8986444
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] 0.8815667
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] 0.6586125
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] 0.8559625
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] 0.8673437
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] 0.8355187
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] 0.6258469
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] 0.9129794
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] 0.7513251
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] 0.8871105
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 -- Mon Dec  5 23:58:08 2022 
*********************************************** 
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 
 96.599   1.480  98.073 

Example timings

TCC.Rcheck/TCC-Ex.timings

nameusersystemelapsed
ROKU0.010.000.01
TCC-class6.3720.2316.605
TCC0.0070.0010.007
WAD0.1160.0030.120
arab0.0320.0040.035
calcAUCValue1.9710.0682.038
calcNormFactors1.0890.0081.097
clusterSample0.2140.0050.219
estimateDE0.4840.0000.484
filterLowCountGenes0.0140.0020.017
getNormalizedData0.2740.0050.278
getResult0.4920.0080.500
hypoData1.6420.0511.694
hypoData_mg1.6600.0041.664
hypoData_ts0.0020.0010.001
makeFCMatrix0.0020.0000.002
nakai0.0310.0000.031
plot.TCC4.2780.0474.325
plotFCPseudocolor4.3490.1124.461
simulateReadCounts4.8990.0324.931