Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:48 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 statTarget on merida1


To the developers/maintainers of the statTarget package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/statTarget.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 1938/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
statTarget 1.26.0  (landing page)
Hemi Luan
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/statTarget
git_branch: RELEASE_3_15
git_last_commit: 2363042
git_last_commit_date: 2022-04-26 11:36:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: statTarget
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings statTarget_1.26.0.tar.gz
StartedAt: 2022-10-19 08:36:33 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 08:37:54 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 80.8 seconds
RetCode: 0
Status:   OK  
CheckDir: statTarget.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings statTarget_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/statTarget.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.26.0’
* 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 ... OK
* 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’
sploe: no visible binding for global variable ‘env’
Undefined global functions or variables:
  Beta.NA GiniImportance dnorm env model.matrix p.value qqline qqnorm
  relevel
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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/statTarget.Rcheck/00check.log’
for details.



Installation output

statTarget.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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)
> #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: Wed Oct 19 08:37:41 2022 

* Step 1: Data File Checking Start..., Time:  Wed Oct 19 08:37:41 2022 

 Data Link 
 metaFile: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/statTarget/extdata/MTBLS79_sampleList.csv 
 profileFile: /Library/Frameworks/R.framework/Versions/4.2/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:  Wed Oct 19 08:37:41 2022 

 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%) Wed Oct 19 08:37:45 2022 

 No. of removed features: 1
 Feature name: 386.21715 

 Output Link: /Users/biocbuild/bbs-3.15-bioc/meat/statTarget.Rcheck/tests 

 Correction Finished! Time:  Wed Oct 19 08:37:45 2022 

 #################################### 
 # Software Version: statTarget 2.0 + # 
 # Email: luanhm@sustech.edu.cn# 
 #################################### 
Warning message:
In dir.create(dirout.w) :
  '/Users/biocbuild/bbs-3.15-bioc/meat/statTarget.Rcheck/tests/statTarget/shiftCor/RSDresult' already exists
> 
> #test_check("statTarget")
> 
> proc.time()
   user  system elapsed 
  5.003   0.274   5.271 

Example timings

statTarget.Rcheck/statTarget-Ex.timings

nameusersystemelapsed
mdsPlot0.0590.0080.067
predict_RF0.0320.0030.036
pvimPlot0.0830.0080.091
rForest0.0270.0010.028
shiftCor3.1920.1123.319
shiftCor_dQC0.2150.0130.228
statAnalysis1.0410.0691.161