Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).

CHECK results for compcodeR on machv2

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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.28.0.tar.gz
StartedAt: 2021-10-14 17:42:19 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:48:49 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 390.2 seconds
RetCode: 0
Status:   OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
NBPSeq.createRmd         34.751  1.160  35.933
DESeq2.createRmd         31.528  3.777  35.126
NOISeq.prenorm.createRmd 11.221  8.632  18.810
EBSeq.createRmd          11.248  1.052  12.282
baySeq.createRmd          7.651  1.036   8.608
DSS.createRmd             6.955  1.052   7.956
show-compData-method      5.232  0.840   5.986
convertcompDataToList     5.076  0.813   5.803
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck/00check.log’
for details.



Installation output

compcodeR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘compcodeR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (compcodeR)

Tests output

compcodeR.Rcheck/tests/testthat.Rout


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

> 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
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 $ include: logi TRUE
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 $ error  : logi TRUE
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  ordinary text without R code

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  ordinary text without R code

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  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 17:48:09 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 17:48:09 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 
121.188  14.922 134.893 

Example timings

compcodeR.Rcheck/compcodeR-Ex.timings

nameusersystemelapsed
DESeq2.createRmd31.528 3.77735.126
DSS.createRmd6.9551.0527.956
EBSeq.createRmd11.248 1.05212.282
NBPSeq.createRmd34.751 1.16035.933
NOISeq.prenorm.createRmd11.221 8.63218.810
TCC.createRmd3.8030.4964.261
baySeq.createRmd7.6511.0368.608
checkDataObject0.4340.0830.509
checkTableConsistency1.6790.2101.874
check_compData0.4290.0740.494
check_compData_results1.0210.1431.151
compData0.0030.0000.004
convertListTocompData0.0060.0020.007
convertcompDataToList5.0760.8135.803
edgeR.GLM.createRmd1.6560.1891.828
edgeR.exact.createRmd1.0690.1291.186
generateCodeHTMLs0.9830.1341.107
generateSyntheticData0.4360.0700.498
listcreateRmd0.0130.0010.013
logcpm.limma.createRmd0.7580.1230.870
runComparison1.5550.1981.737
runComparisonGUI0.0010.0000.001
runDiffExp1.0490.1461.182
show-compData-method5.2320.8405.986
sqrtcpm.limma.createRmd0.7690.1260.883
summarizeSyntheticDataSet0.4140.0720.477
ttest.createRmd0.7870.1200.896
voom.limma.createRmd0.9590.1271.074
voom.ttest.createRmd0.8330.1260.947