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CHECK report for statTarget on machv2

This page was generated on 2020-10-17 11:59:43 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE statTarget PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1745/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
statTarget 1.18.0
Hemi Luan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/statTarget
Branch: RELEASE_3_11
Last Commit: b80b7d4
Last Changed Date: 2020-04-27 15:02:20 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: statTarget
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings statTarget_1.18.0.tar.gz
StartedAt: 2020-10-17 05:41:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:43:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 68.6 seconds
RetCode: 0
Status:  OK 
CheckDir: statTarget.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings statTarget_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/statTarget.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘statTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘statTarget’ version ‘1.18.0’
* 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 ‘statTarget’ 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 ... NOTE
'library' or 'require' calls in package code:
  ‘gWidgets2’ ‘gWidgets2RGtk2’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ComBat_qcFree: no visible global function definition for ‘model.matrix’
ComBat_qcFree: no visible binding for global variable ‘Beta.NA’
ComBat_qcFree: no visible global function definition for ‘dnorm’
ComBat_qcFree: no visible global function definition for ‘qqnorm’
ComBat_qcFree: no visible global function definition for ‘qqline’
oddRatio : logit_or: no visible global function definition for
  ‘relevel’
pvimPlot: no visible binding for global variable ‘GiniImportance’
pvimPlot: no visible binding for global variable ‘p.value’
shiftCor_dQC: no visible global function definition for ‘model.matrix’
statTargetGUI: no visible global function definition for ‘svalue<-’
statTargetGUI: no visible global function definition for ‘gexpandgroup’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘galert’
statTargetGUI: no visible global function definition for ‘ggroup’
statTargetGUI: no visible global function definition for ‘gformlayout’
statTargetGUI: no visible global function definition for ‘glayout’
statTargetGUI: no visible global function definition for ‘glabel’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘svalue’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘size<-’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘dispose’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘gwindow’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘gvbox’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘glabel’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘gseparator’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘ggroup’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘addSpring’
statTargetGUI : <anonymous> : <anonymous>: no visible global function
  definition for ‘gbutton’
statTargetGUI : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘dispose’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘gtext’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘gseparator’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘ggroup’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘addSpring’
statTargetGUI : <anonymous>: no visible global function definition for
  ‘gbutton’
transCode : skyline: no visible binding for global variable
  ‘Replicate.Name’
Undefined global functions or variables:
  Beta.NA GiniImportance Replicate.Name addSpring dispose dnorm galert
  gbutton gexpandgroup gformlayout ggroup glabel glayout gseparator
  gtext gvbox gwindow model.matrix p.value qqline qqnorm relevel size<-
  svalue svalue<-
Consider adding
  importFrom("stats", "dnorm", "model.matrix", "qqline", "qqnorm",
             "relevel")
to your NAMESPACE file.
* 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
* 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-3.11-bioc/meat/statTarget.Rcheck/00check.log’
for details.



Installation output

statTarget.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘statTarget’ ...
** 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 (statTarget)

Tests output

statTarget.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(statTarget)

Use 'statTargetGUI()' to start the GUI program. For details see https://stattarget.github.io.

> #library(statTarget)
> datpath <- system.file("extdata",package = "statTarget")
> samPeno <- paste(datpath,"MTBLS79_sampleList.csv", sep="/")
> samFile <- paste(datpath,"MTBLS79.csv", sep="/")
> file <- paste(datpath,"data_example_two_groups.csv", sep="/")
> #statAnalysis(file, Frule = 0.8,imputeM = "KNN", glog = TRUE, test.multi=TRUE, nvarRF =10, scaling = "Pareto",silt = 500, pcax = 1, pcay = 2) 
> shiftCor(samPeno,samFile,Frule = 0.8,QCspan = 0.75, degree = 2,imputeM = "KNN")

statTarget: Signal Correction Start... Time: Sat Oct 17 05:42:50 2020 

* Step 1: Data File Checking Start..., Time:  Sat Oct 17 05:42:50 2020 

 Data Link 
 metaFile: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/statTarget/extdata/MTBLS79_sampleList.csv 
 profileFile: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/statTarget/extdata/MTBLS79.csv 

 172 Meta Samples vs 172 Profile samples
 The Meta samples list (*NA, missing data from the Profile File)

  [1] "batch01_QC01" "batch01_QC02" "batch01_QC03" "batch01_C05"  "batch01_S07" 
  [6] "batch01_C10"  "batch01_QC04" "batch01_S01"  "batch01_C03"  "batch01_S05" 
 [11] "batch01_C07"  "batch01_S06"  "batch01_QC05" "batch01_C08"  "batch01_C06" 
 [16] "batch01_S02"  "batch01_S09"  "batch01_QC06" "batch01_S04"  "batch01_C04" 
 [21] "batch01_S10"  "batch01_C09"  "batch01_QC07" "batch02_C05"  "batch02_S03" 
 [26] "batch02_S07"  "batch02_C01"  "batch02_C10"  "batch02_QC08" "batch02_S01" 
 [31] "batch02_C03"  "batch02_S05"  "batch02_C07"  "batch02_S06"  "batch02_QC09"
 [36] "batch02_C08"  "batch02_C06"  "batch02_S02"  "batch02_S09"  "batch02_C02" 
 [41] "batch02_QC10" "batch02_S04"  "batch02_S08"  "batch02_C04"  "batch02_S10" 
 [46] "batch02_C09"  "batch02_QC11" "batch03_C05"  "batch03_S03"  "batch03_S07" 
 [51] "batch03_C01"  "batch03_C10"  "batch03_QC12" "batch03_S01"  "batch03_C03" 
 [56] "batch03_S05"  "batch03_C07"  "batch03_S06"  "batch03_QC13" "batch03_C08" 
 [61] "batch03_C06"  "batch03_S02"  "batch03_S09"  "batch03_C02"  "batch03_QC14"
 [66] "batch03_S04"  "batch03_S08"  "batch03_C04"  "batch03_S10"  "batch03_C09" 
 [71] "batch03_QC15" "batch04_C05"  "batch04_S03"  "batch04_S07"  "batch04_C01" 
 [76] "batch04_QC16" "batch04_S01"  "batch04_S05"  "batch04_C07"  "batch04_S06" 
 [81] "batch04_QC17" "batch04_C08"  "batch04_C06"  "batch04_S02"  "batch04_S09" 
 [86] "batch04_C02"  "batch04_QC18" "batch04_S08"  "batch04_C04"  "batch04_S10" 
 [91] "batch04_QC19" "batch05_QC20" "batch05_S03"  "batch05_S07"  "batch05_C01" 
 [96] "batch05_C10"  "batch05_QC21" "batch05_S01"  "batch05_C03"  "batch05_C07" 
[101] "batch05_QC22" "batch05_C06"  "batch05_C02"  "batch05_QC23" "batch05_S04" 
[106] "batch05_S08"  "batch05_C04"  "batch05_QC24" "batch06_QC25" "batch06_S03" 
[111] "batch06_C10"  "batch06_QC26" "batch06_S01"  "batch06_C03"  "batch06_S05" 
[116] "batch06_C07"  "batch06_S06"  "batch06_QC27" "batch06_C08"  "batch06_C06" 
[121] "batch06_S02"  "batch06_C02"  "batch06_QC28" "batch06_S04"  "batch06_S08" 
[126] "batch06_C04"  "batch06_C09"  "batch06_QC29" "batch07_QC30" "batch07_C05" 
[131] "batch07_S03"  "batch07_S07"  "batch07_C01"  "batch07_C10"  "batch07_QC31"
[136] "batch07_C03"  "batch07_S05"  "batch07_C07"  "batch07_S06"  "batch07_QC32"
[141] "batch07_C08"  "batch07_S02"  "batch07_S09"  "batch07_C02"  "batch07_QC33"
[146] "batch07_S04"  "batch07_S08"  "batch07_S10"  "batch07_C09"  "batch07_QC34"
[151] "batch08_C05"  "batch08_S03"  "batch08_S07"  "batch08_C01"  "batch08_C10" 
[156] "batch08_QC36" "batch08_S01"  "batch08_C03"  "batch08_S05"  "batch08_C07" 
[161] "batch08_S06"  "batch08_QC37" "batch08_C08"  "batch08_S02"  "batch08_S09" 
[166] "batch08_QC38" "batch08_S04"  "batch08_S08"  "batch08_C04"  "batch08_S10" 
[171] "batch08_C09"  "batch08_QC39"

 Meta-information: 

  Class No.
1     1  66
2     2  68
3    QC  38
  Batch No.
1     1  91
2     2  17
3     3  20
4     4  44

 Metabolic profile information: 

               no.
QC and samples 172
Metabolites     48

* Step 2: Evaluation of Missing Value... 

 The number of missing value before QC based signal correction:  336
 The number of filtered variables using the modified  80 % rule :   6 

* Step 3: Imputation start... 

 The imputation method was set at 'KNN'
 The number of missing value after imputation:  0
 Imputation Finished! 
 
* Step 4: QC-based Signal Correction Start... Time:  Sat Oct 17 05:42:50 2020 

 The Signal Correction method was set at QC-RFSC 

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 Calculation of CV distribution of raw peaks (QC)...

            CV<5%   CV<10%   CV<15%   CV<20%   CV<25%   CV<30%   CV<35%
Batch_1  4.761905 50.00000 71.42857 78.57143 85.71429 92.85714 95.23810
Batch_2 21.428571 69.04762 80.95238 80.95238 92.85714 95.23810 95.23810
Batch_3 11.904762 45.23810 78.57143 83.33333 85.71429 92.85714 97.61905
Batch_4  7.142857 64.28571 78.57143 83.33333 92.85714 92.85714 95.23810
Total    0.000000 19.04762 38.09524 66.66667 69.04762 78.57143 80.95238
           CV<40%    CV<45%    CV<50%    CV<55%    CV<60% CV<65% CV<70% CV<75%
Batch_1  95.23810  97.61905 100.00000 100.00000 100.00000    100    100    100
Batch_2  95.23810  95.23810  97.61905  97.61905  97.61905    100    100    100
Batch_3  97.61905 100.00000 100.00000 100.00000 100.00000    100    100    100
Batch_4 100.00000 100.00000 100.00000 100.00000 100.00000    100    100    100
Total    80.95238  85.71429  88.09524  95.23810 100.00000    100    100    100
        CV<80% CV<85% CV<90% CV<95% CV<100%
Batch_1    100    100    100    100     100
Batch_2    100    100    100    100     100
Batch_3    100    100    100    100     100
Batch_4    100    100    100    100     100
Total      100    100    100    100     100

 Calculation of CV distribution of corrected peaks (QC)...

           CV<5%   CV<10%   CV<15%   CV<20%   CV<25%    CV<30%    CV<35%
Batch_1 45.23810 76.19048 85.71429 92.85714  95.2381  95.23810 100.00000
Batch_2 40.47619 78.57143 85.71429 92.85714  95.2381  95.23810  95.23810
Batch_3 11.90476 66.66667 80.95238 88.09524  95.2381  97.61905  97.61905
Batch_4 30.95238 73.80952 85.71429 97.61905 100.0000 100.00000 100.00000
Total   26.19048 73.80952 90.47619 95.23810  95.2381  97.61905 100.00000
           CV<40% CV<45% CV<50% CV<55% CV<60% CV<65% CV<70% CV<75% CV<80%
Batch_1 100.00000    100    100    100    100    100    100    100    100
Batch_2  97.61905    100    100    100    100    100    100    100    100
Batch_3 100.00000    100    100    100    100    100    100    100    100
Batch_4 100.00000    100    100    100    100    100    100    100    100
Total   100.00000    100    100    100    100    100    100    100    100
        CV<85% CV<90% CV<95% CV<100%
Batch_1    100    100    100     100
Batch_2    100    100    100     100
Batch_3    100    100    100     100
Batch_4    100    100    100     100
Total      100    100    100     100

* Step 5:  Removal of the features (CV% > 30%) Sat Oct 17 05:42:53 2020 

 No. of removed features: 1
 Feature name: 386.21715 

 Output Link: /Users/biocbuild/bbs-3.11-bioc/meat/statTarget.Rcheck/tests 

 Correction Finished! Time:  Sat Oct 17 05:42:53 2020 

 #################################### 
 # Software Version: statTarget 2.0 + # 
 #################################### 
Warning message:
In dir.create(dirout.w) :
  '/Users/biocbuild/bbs-3.11-bioc/meat/statTarget.Rcheck/tests/statTarget/shiftCor/RSDresult' already exists
> 
> #test_check("statTarget")
> 
> proc.time()
   user  system elapsed 
  4.306   0.315   4.598 

Example timings

statTarget.Rcheck/statTarget-Ex.timings

nameusersystemelapsed
mdsPlot0.0460.0060.054
predict_RF0.0330.0040.037
pvimPlot0.0830.0060.091
rForest0.0270.0010.028
shiftCor2.8360.1532.993
shiftCor_dQC0.2210.0220.243
statAnalysis0.9600.0891.103
statTargetGUI0.0000.0010.001
transX0.0130.0030.017