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CHECK report for compcodeR on merida1

This page was generated on 2021-05-06 12:34:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the compcodeR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 359/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.26.1  (landing page)
Charlotte Soneson
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/compcodeR
Branch: RELEASE_3_12
Last Commit: b692f6a
Last Changed Date: 2020-11-08 11:24:58 -0400 (Sun, 08 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  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    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.26.1
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_1.26.1.tar.gz
StartedAt: 2021-05-06 00:32:48 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:38:59 -0400 (Thu, 06 May 2021)
EllapsedTime: 371.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: compcodeR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.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 ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.26.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘compcodeR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' call to ‘rpanel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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         36.953  1.074  38.114
DESeq2.createRmd         23.909  2.871  26.671
NOISeq.prenorm.createRmd 10.758  8.737  18.763
EBSeq.createRmd           9.015  0.888   9.907
show-compData-method      7.150  0.956   8.031
DSS.createRmd             6.916  0.998   7.896
convertcompDataToList     6.495  0.972   7.423
baySeq.createRmd          5.731  0.964   6.681
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.Rcheck/00check.log’
for details.



Installation output

compcodeR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘compcodeR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
** testing if installed package keeps a record of temporary installation path
* DONE (compcodeR)

Tests output

compcodeR.Rcheck/tests/testthat.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.

> library(testthat)
> library(compcodeR)
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Warning message:
replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR' 
> 
> 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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 $ 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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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.1.30.0.median on Thu May  6 00:38:23 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.1.30.0.median on Thu May  6 00:38:23 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 
103.412  14.476 117.172 

Example timings

compcodeR.Rcheck/compcodeR-Ex.timings

nameusersystemelapsed
DESeq2.createRmd23.909 2.87126.671
DSS.createRmd6.9160.9987.896
EBSeq.createRmd9.0150.8889.907
NBPSeq.createRmd36.953 1.07438.114
NOISeq.prenorm.createRmd10.758 8.73718.763
TCC.createRmd3.2070.4333.650
baySeq.createRmd5.7310.9646.681
checkDataObject0.5110.0930.600
checkTableConsistency1.6690.2271.917
check_compData0.5590.0850.639
check_compData_results1.1110.1591.263
compData0.0020.0000.003
convertListTocompData0.0050.0020.007
convertcompDataToList6.4950.9727.423
edgeR.GLM.createRmd1.5960.1991.787
edgeR.exact.createRmd1.1790.1591.340
generateCodeHTMLs1.0930.1501.237
generateSyntheticData0.5880.0850.667
listcreateRmd0.0130.0000.014
logcpm.limma.createRmd0.9370.1371.064
runComparison1.7430.2021.933
runComparisonGUI0.0010.0000.002
runDiffExp1.1200.1461.256
show-compData-method7.1500.9568.031
sqrtcpm.limma.createRmd0.8990.1351.025
summarizeSyntheticDataSet0.5820.0860.661
ttest.createRmd0.9330.1361.060
voom.limma.createRmd1.0280.1451.171
voom.ttest.createRmd0.8790.1381.013