Hemi Luan
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/statTarget |
| Branch: RELEASE_3_10 |
| Last Commit: e70a4b3 |
| Last Changed Date: 2019-10-30 02:38:12 -0400 (Wed, 30 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:55 -0400 (Wed, 15 Apr 2020).
| Package 1674/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| statTarget 1.16.1 Hemi Luan
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: statTarget |
| Version: 1.16.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:statTarget.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings statTarget_1.16.1.tar.gz |
| StartedAt: 2020-04-15 04:13:56 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:14:43 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 47.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: statTarget.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:statTarget.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings statTarget_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/statTarget.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.1’
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/statTarget.Rcheck/00check.log’
for details.
statTarget.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL statTarget ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Apr 15 04:14:38 2020
* Step 1: Data File Checking Start..., Time: Wed Apr 15 04:14:38 2020
Data Link
metaFile: /home/biocbuild/bbs-3.10-bioc/R/library/statTarget/extdata/MTBLS79_sampleList.csv
profileFile: /home/biocbuild/bbs-3.10-bioc/R/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 Apr 15 04:14:38 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
Output Link: /home/biocbuild/bbs-3.10-bioc/meat/statTarget.Rcheck/tests
Correction Finished! Time: Wed Apr 15 04:14:41 2020
####################################
# Software Version: statTarget 2.0 #
####################################
Warning message:
In dir.create(dirout.w) :
'/home/biocbuild/bbs-3.10-bioc/meat/statTarget.Rcheck/tests/statTarget/shiftCor/RSDresult' already exists
>
> #test_check("statTarget")
>
> proc.time()
user system elapsed
3.436 0.096 3.577
statTarget.Rcheck/statTarget-Ex.timings
| name | user | system | elapsed | |
| mdsPlot | 0.056 | 0.004 | 0.069 | |
| predict_RF | 0.028 | 0.000 | 0.031 | |
| pvimPlot | 0.072 | 0.008 | 0.081 | |
| rForest | 0.024 | 0.000 | 0.023 | |
| shiftCor | 2.548 | 0.024 | 2.601 | |
| shiftCor_dQC | 0.248 | 0.000 | 0.248 | |
| statAnalysis | 0.684 | 0.020 | 0.708 | |
| statTargetGUI | 0 | 0 | 0 | |
| transX | 0.008 | 0.004 | 0.014 | |