Hemi Luan
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/statTarget |
| Branch: RELEASE_3_9 |
| Last Commit: 4b53990 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:51 -0400 (Wed, 16 Oct 2019).
| Package 1597/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| statTarget 1.14.0 Hemi Luan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: statTarget |
| Version: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2019-10-16 07:11:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:13:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 76.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: statTarget.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/statTarget.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’ * 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’ 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 :: 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 : : no visible global function definition for ‘svalue’ statTargetGUI : : no visible global function definition for ‘size<-’ statTargetGUI : : : no visible global function definition for ‘dispose’ statTargetGUI : : : no visible global function definition for ‘gwindow’ statTargetGUI : : : no visible global function definition for ‘gvbox’ statTargetGUI : : : no visible global function definition for ‘glabel’ statTargetGUI : : : no visible global function definition for ‘gseparator’ statTargetGUI : : : no visible global function definition for ‘ggroup’ statTargetGUI : : : no visible global function definition for ‘addSpring’ statTargetGUI : : : no visible global function definition for ‘gbutton’ statTargetGUI : : : : no visible global function definition for ‘dispose’ statTargetGUI : : no visible global function definition for ‘gtext’ statTargetGUI : : no visible global function definition for ‘gseparator’ statTargetGUI : : no visible global function definition for ‘ggroup’ statTargetGUI : : no visible global function definition for ‘addSpring’ statTargetGUI : : 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 size<- svalue svalue<- Consider adding importFrom("stats", "dnorm", "model.matrix", "qqline", "qqnorm") 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-3.9-bioc/meat/statTarget.Rcheck/00check.log’ for details.
statTarget.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL statTarget ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
statTarget.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: Wed Oct 16 07:13:04 2019
* Step 1: Data File Checking Start..., Time: Wed Oct 16 07:13:04 2019
Data Link
metaFile: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/statTarget/extdata/MTBLS79_sampleList.csv
profileFile: /Library/Frameworks/R.framework/Versions/3.6/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 16 07:13:04 2019
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
Output Link: /Users/biocbuild/bbs-3.9-bioc/meat/statTarget.Rcheck/tests
Correction Finished! Time: Wed Oct 16 07:13:07 2019
####################################
# Software Version: statTarget 2.0 #
####################################
Warning message:
In dir.create(dirout.w) :
'/Users/biocbuild/bbs-3.9-bioc/meat/statTarget.Rcheck/tests/statTarget/shiftCor/RSDresult' already exists
>
> #test_check("statTarget")
>
> proc.time()
user system elapsed
4.441 0.504 5.006
statTarget.Rcheck/statTarget-Ex.timings
| name | user | system | elapsed | |
| mdsPlot | 0.071 | 0.020 | 0.093 | |
| predict_RF | 0.033 | 0.007 | 0.041 | |
| pvimPlot | 0.075 | 0.017 | 0.091 | |
| rForest | 0.034 | 0.008 | 0.043 | |
| shiftCor | 2.751 | 0.241 | 2.995 | |
| shiftCor_dQC | 0.232 | 0.027 | 0.259 | |
| statAnalysis | 1.051 | 0.108 | 1.163 | |
| statTargetGUI | 0.000 | 0.000 | 0.001 | |
| transX | 0.015 | 0.004 | 0.021 | |