Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).

CHECK results for compcodeR on tokay2

To the developers/maintainers of the compcodeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compcodeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 369/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.28.0  (landing page)
Charlotte Soneson
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/compcodeR
git_branch: RELEASE_3_13
git_last_commit: 16b062e
git_last_commit_date: 2021-05-19 12:04:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: compcodeR
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compcodeR_1.28.0.tar.gz
StartedAt: 2021-10-14 21:27:56 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:35:46 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 469.8 seconds
RetCode: 0
Status:   OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compcodeR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.28.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rpanel'
* 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 'compcodeR' 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
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
NBPSeq.createRmd 53.53   0.67   54.24
DESeq2.createRmd 19.82   1.09   20.93
EBSeq.createRmd  14.50   0.61   15.15
DSS.createRmd     4.84   0.29    5.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
NBPSeq.createRmd 48.25   0.58   48.83
DESeq2.createRmd 19.74   0.65   20.41
EBSeq.createRmd  12.22   0.07   12.30
DSS.createRmd     4.88   0.18    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck/00check.log'
for details.



Installation output

compcodeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/compcodeR_1.28.0.tar.gz && rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compcodeR.buildbin-libdir compcodeR_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL compcodeR_1.28.0.zip && rm compcodeR_1.28.0.tar.gz compcodeR_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 45 2347k   45 1065k    0     0  1623k      0  0:00:01 --:--:--  0:00:01 1623k
100 2347k  100 2347k    0     0  2053k      0  0:00:01  0:00:01 --:--:-- 2055k

install for i386

* installing *source* package 'compcodeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'compcodeR'
    finding HTML links ... done
    DESeq2.createRmd                        html  
    DSS.createRmd                           html  
    EBSeq.createRmd                         html  
    NBPSeq.createRmd                        html  
    NOISeq.prenorm.createRmd                html  
    TCC.createRmd                           html  
    baySeq.createRmd                        html  
    checkDataObject                         html  
    checkTableConsistency                   html  
    check_compData                          html  
    check_compData_results                  html  
    compData-class                          html  
    compData                                html  
    compcodeR-package                       html  
    convertListTocompData                   html  
    convertcompDataToList                   html  
    edgeR.GLM.createRmd                     html  
    edgeR.exact.createRmd                   html  
    generateCodeHTMLs                       html  
    generateSyntheticData                   html  
    listcreateRmd                           html  
    logcpm.limma.createRmd                  html  
    runComparison                           html  
    runComparisonGUI                        html  
    runDiffExp                              html  
    show-compData-method                    html  
    sqrtcpm.limma.createRmd                 html  
    summarizeSyntheticDataSet               html  
    ttest.createRmd                         html  
    voom.limma.createRmd                    html  
    voom.ttest.createRmd                    html  
** 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

install for x64

* installing *source* package 'compcodeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.28.0.zip
* DONE (compcodeR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'compcodeR' successfully unpacked and MD5 sums checked

Tests output

compcodeR.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(compcodeR)
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
> 
> test_check("compcodeR")
  ordinary text without R code

label: settings (with options) 
List of 1
 $ echo: logi FALSE

label: modifications (with options) 
List of 1
 $ echo: logi FALSE

label: calcma (with options) 
List of 4
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE

  ordinary text without R code

label: maplot-trueDEstatus (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: maplot-nbroutliers (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: logfoldchanges (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

 [1] "DESeq2.createRmd"         "DSS.createRmd"           
 [3] "EBSeq.createRmd"          "NBPSeq.createRmd"        
 [5] "NOISeq.prenorm.createRmd" "TCC.createRmd"           
 [7] "baySeq.createRmd"         "edgeR.GLM.createRmd"     
 [9] "edgeR.exact.createRmd"    "logcpm.limma.createRmd"  
[11] "sqrtcpm.limma.createRmd"  "ttest.createRmd"         
[13] "voom.limma.createRmd"     "voom.ttest.createRmd"    
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi TRUE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi TRUE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi TRUE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
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 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
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 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
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 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
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 $ error  : logi TRUE
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  ordinary text without R code

label: unnamed-chunk-1 (with options) 
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 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
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 $ error  : logi TRUE
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  ordinary text without R code

label: unnamed-chunk-1 (with options) 
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 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

An object of class compData 
Dataset name: B_625_625 
Number of samples: 10 
Number of variables: 500 
Number of random outliers: 0 
Number of single outliers: 0 
Number of known truly differentially expressed genes: 50 
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 21:34:14 2021 . 

count.matrix:
   sample1 sample2 sample3 sample4 sample5 sample6
g1       4       8       5       2       8       8
g2     314     419     186     172     294     133
g3    1030    1583    1011    1033     747    1291
g4       0       1       1       0       2       2
g5      48     122     215      62     106      90
g6      27      16      18      44      29      74
+ 494 rows and 4 cols...

sample.annotations:
        condition depth.factor
sample1         1    1.1049378
sample2         1    1.2875127
sample3         1    1.1581115
sample4         1    1.3611698
sample5         1    1.0581603
sample6         2    0.7594447
+ 4 rows...

variable.annotations:
   truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1         0.11610054         0.11610054     6.878049    16.363472
g2         0.43796296         0.43796296   303.073171   893.165617
g3         0.04321133         0.04321133  1223.414634  2760.990905
g4         0.55624371         0.55624371     0.902439     6.153083
g5         0.15968189         0.15968189   148.146341   316.915193
g6         0.36378999         0.36378999    40.439024   132.785087
   n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1                       0                       0                         0
g2                       0                       0                         0
g3                       0                       0                         0
g4                       0                       0                         0
g5                       0                       0                         0
g6                       0                       0                         0
   n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1                         0                       0                       0
g2                         0                       0                       0
g3                         0                       0                       0
g4                         0                       0                       0
g5                         0                       0                       0
g6                         0                       0                       0
   n.single.outliers.down.S1 n.single.outliers.down.S2  M.value    A.value
g1                         0                         0 1.158386  2.9291506
g2                         0                         0 1.349570  8.6365105
g3                         0                         0 1.050582 10.4859190
g4                         0                         0 1.432447  0.7393097
g5                         0                         0 1.185233  7.1150497
g6                         0                         0 2.176450  5.6916570
   truelog2foldchanges upregulation downregulation differential.expression
g1            1.250408            1              0                       1
g2            1.559262            1              0                       1
g3            1.174273            1              0                       1
g4            2.769408            1              0                       1
g5            1.097074            1              0                       1
g6            1.715273            1              0                       1
+ 494 rows...

Differential expression results:

            FDR         lfdr     score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...

An object of class compData 
Dataset name: B_625_625 
Number of samples: 4 
Number of variables: 500 
Number of random outliers: 0 
Number of single outliers: 0 
Number of known truly differentially expressed genes: 50 
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 21:34:14 2021 . 

count.matrix:
   sample1 sample2 sample3 sample4
g1       4       8       5       2
g2     314     419     186     172
g3    1030    1583    1011    1033
g4       0       1       1       0
g5      48     122     215      62
g6      27      16      18      44
+ 494 rows...

sample.annotations:
        condition depth.factor
sample1         1    1.1049378
sample2         1    1.2875127
sample3         1    1.1581115
sample4         1    1.3611698
sample5         1    1.0581603
sample6         2    0.7594447
+ 4 rows...

variable.annotations:
   truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1         0.11610054         0.11610054     6.878049    16.363472
g2         0.43796296         0.43796296   303.073171   893.165617
g3         0.04321133         0.04321133  1223.414634  2760.990905
g4         0.55624371         0.55624371     0.902439     6.153083
g5         0.15968189         0.15968189   148.146341   316.915193
g6         0.36378999         0.36378999    40.439024   132.785087
   n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1                       0                       0                         0
g2                       0                       0                         0
g3                       0                       0                         0
g4                       0                       0                         0
g5                       0                       0                         0
g6                       0                       0                         0
   n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1                         0                       0                       0
g2                         0                       0                       0
g3                         0                       0                       0
g4                         0                       0                       0
g5                         0                       0                       0
g6                         0                       0                       0
   n.single.outliers.down.S1 n.single.outliers.down.S2  M.value    A.value
g1                         0                         0 1.158386  2.9291506
g2                         0                         0 1.349570  8.6365105
g3                         0                         0 1.050582 10.4859190
g4                         0                         0 1.432447  0.7393097
g5                         0                         0 1.185233  7.1150497
g6                         0                         0 2.176450  5.6916570
   truelog2foldchanges upregulation downregulation differential.expression
g1            1.250408            1              0                       1
g2            1.559262            1              0                       1
g3            1.174273            1              0                       1
g4            2.769408            1              0                       1
g5            1.097074            1              0                       1
g6            1.715273            1              0                       1
+ 494 rows...

Differential expression results:

            FDR         lfdr     score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ]
> 
> proc.time()
   user  system elapsed 
  64.65    3.87   68.78 

compcodeR.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(compcodeR)
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
> 
> test_check("compcodeR")
  ordinary text without R code

label: settings (with options) 
List of 1
 $ echo: logi FALSE

label: modifications (with options) 
List of 1
 $ echo: logi FALSE

label: calcma (with options) 
List of 4
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE

  ordinary text without R code

label: maplot-trueDEstatus (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: maplot-nbroutliers (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

label: logfoldchanges (with options) 
List of 7
 $ echo   : logi FALSE
 $ dev    : chr "png"
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

 [1] "DESeq2.createRmd"         "DSS.createRmd"           
 [3] "EBSeq.createRmd"          "NBPSeq.createRmd"        
 [5] "NOISeq.prenorm.createRmd" "TCC.createRmd"           
 [7] "baySeq.createRmd"         "edgeR.GLM.createRmd"     
 [9] "edgeR.exact.createRmd"    "logcpm.limma.createRmd"  
[11] "sqrtcpm.limma.createRmd"  "ttest.createRmd"         
[13] "voom.limma.createRmd"     "voom.ttest.createRmd"    
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi TRUE
 $ error  : logi TRUE
 $ warning: logi TRUE

  ordinary text without R code

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An object of class compData 
Dataset name: B_625_625 
Number of samples: 10 
Number of variables: 500 
Number of random outliers: 0 
Number of single outliers: 0 
Number of known truly differentially expressed genes: 50 
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 21:35:20 2021 . 

count.matrix:
   sample1 sample2 sample3 sample4 sample5 sample6
g1       4       8       5       2       8       8
g2     314     419     186     172     294     133
g3    1030    1583    1011    1033     747    1291
g4       0       1       1       0       2       2
g5      48     122     215      62     106      90
g6      27      16      18      44      29      74
+ 494 rows and 4 cols...

sample.annotations:
        condition depth.factor
sample1         1    1.1049378
sample2         1    1.2875127
sample3         1    1.1581115
sample4         1    1.3611698
sample5         1    1.0581603
sample6         2    0.7594447
+ 4 rows...

variable.annotations:
   truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1         0.11610054         0.11610054     6.878049    16.363472
g2         0.43796296         0.43796296   303.073171   893.165617
g3         0.04321133         0.04321133  1223.414634  2760.990905
g4         0.55624371         0.55624371     0.902439     6.153083
g5         0.15968189         0.15968189   148.146341   316.915193
g6         0.36378999         0.36378999    40.439024   132.785087
   n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1                       0                       0                         0
g2                       0                       0                         0
g3                       0                       0                         0
g4                       0                       0                         0
g5                       0                       0                         0
g6                       0                       0                         0
   n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1                         0                       0                       0
g2                         0                       0                       0
g3                         0                       0                       0
g4                         0                       0                       0
g5                         0                       0                       0
g6                         0                       0                       0
   n.single.outliers.down.S1 n.single.outliers.down.S2  M.value    A.value
g1                         0                         0 1.158386  2.9291506
g2                         0                         0 1.349570  8.6365105
g3                         0                         0 1.050582 10.4859190
g4                         0                         0 1.432447  0.7393097
g5                         0                         0 1.185233  7.1150497
g6                         0                         0 2.176450  5.6916570
   truelog2foldchanges upregulation downregulation differential.expression
g1            1.250408            1              0                       1
g2            1.559262            1              0                       1
g3            1.174273            1              0                       1
g4            2.769408            1              0                       1
g5            1.097074            1              0                       1
g6            1.715273            1              0                       1
+ 494 rows...

Differential expression results:

            FDR         lfdr     score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...

An object of class compData 
Dataset name: B_625_625 
Number of samples: 4 
Number of variables: 500 
Number of random outliers: 0 
Number of single outliers: 0 
Number of known truly differentially expressed genes: 50 
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 21:35:20 2021 . 

count.matrix:
   sample1 sample2 sample3 sample4
g1       4       8       5       2
g2     314     419     186     172
g3    1030    1583    1011    1033
g4       0       1       1       0
g5      48     122     215      62
g6      27      16      18      44
+ 494 rows...

sample.annotations:
        condition depth.factor
sample1         1    1.1049378
sample2         1    1.2875127
sample3         1    1.1581115
sample4         1    1.3611698
sample5         1    1.0581603
sample6         2    0.7594447
+ 4 rows...

variable.annotations:
   truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1         0.11610054         0.11610054     6.878049    16.363472
g2         0.43796296         0.43796296   303.073171   893.165617
g3         0.04321133         0.04321133  1223.414634  2760.990905
g4         0.55624371         0.55624371     0.902439     6.153083
g5         0.15968189         0.15968189   148.146341   316.915193
g6         0.36378999         0.36378999    40.439024   132.785087
   n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1                       0                       0                         0
g2                       0                       0                         0
g3                       0                       0                         0
g4                       0                       0                         0
g5                       0                       0                         0
g6                       0                       0                         0
   n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1                         0                       0                       0
g2                         0                       0                       0
g3                         0                       0                       0
g4                         0                       0                       0
g5                         0                       0                       0
g6                         0                       0                       0
   n.single.outliers.down.S1 n.single.outliers.down.S2  M.value    A.value
g1                         0                         0 1.158386  2.9291506
g2                         0                         0 1.349570  8.6365105
g3                         0                         0 1.050582 10.4859190
g4                         0                         0 1.432447  0.7393097
g5                         0                         0 1.185233  7.1150497
g6                         0                         0 2.176450  5.6916570
   truelog2foldchanges upregulation downregulation differential.expression
g1            1.250408            1              0                       1
g2            1.559262            1              0                       1
g3            1.174273            1              0                       1
g4            2.769408            1              0                       1
g5            1.097074            1              0                       1
g6            1.715273            1              0                       1
+ 494 rows...

Differential expression results:

            FDR         lfdr     score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ]
> 
> proc.time()
   user  system elapsed 
  62.90    1.81   64.93 

Example timings

compcodeR.Rcheck/examples_i386/compcodeR-Ex.timings

nameusersystemelapsed
DESeq2.createRmd19.82 1.0920.93
DSS.createRmd4.840.295.18
EBSeq.createRmd14.50 0.6115.15
NBPSeq.createRmd53.53 0.6754.24
NOISeq.prenorm.createRmd3.210.123.33
TCC.createRmd2.700.333.22
baySeq.createRmd4.230.174.41
checkDataObject0.210.110.31
checkTableConsistency1.090.311.41
check_compData0.170.000.17
check_compData_results0.550.140.69
compData000
convertListTocompData000
convertcompDataToList2.760.052.81
edgeR.GLM.createRmd1.290.031.31
edgeR.exact.createRmd0.790.020.81
generateCodeHTMLs0.500.050.55
generateSyntheticData0.170.000.17
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.360.060.42
runComparison1.000.091.09
runComparisonGUI000
runDiffExp0.520.030.55
show-compData-method2.410.002.40
sqrtcpm.limma.createRmd0.480.080.56
summarizeSyntheticDataSet0.330.000.33
ttest.createRmd0.440.080.52
voom.limma.createRmd0.530.050.58
voom.ttest.createRmd0.580.030.61

compcodeR.Rcheck/examples_x64/compcodeR-Ex.timings

nameusersystemelapsed
DESeq2.createRmd19.74 0.6520.41
DSS.createRmd4.880.185.08
EBSeq.createRmd12.22 0.0712.30
NBPSeq.createRmd48.25 0.5848.83
NOISeq.prenorm.createRmd3.780.244.02
TCC.createRmd2.580.032.60
baySeq.createRmd3.830.033.86
checkDataObject0.200.000.21
checkTableConsistency1.220.091.31
check_compData0.190.000.19
check_compData_results0.560.000.56
compData0.020.000.02
convertListTocompData000
convertcompDataToList2.230.002.23
edgeR.GLM.createRmd1.030.001.03
edgeR.exact.createRmd0.720.020.74
generateCodeHTMLs0.520.030.54
generateSyntheticData0.180.000.19
listcreateRmd000
logcpm.limma.createRmd0.390.030.42
runComparison1.000.031.03
runComparisonGUI000
runDiffExp0.540.000.53
show-compData-method3.140.003.14
sqrtcpm.limma.createRmd0.410.030.44
summarizeSyntheticDataSet0.170.000.17
ttest.createRmd0.410.020.42
voom.limma.createRmd0.490.020.50
voom.ttest.createRmd0.450.000.48