Hemi Luan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/statTarget |
| Branch: RELEASE_3_6 |
| Last Commit: f77db83 |
| Last Changed Date: 2017-10-30 12:41:22 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:45 -0400 (Thu, 12 Apr 2018).
| Package 1359/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| statTarget 1.8.0 Hemi Luan
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: statTarget |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings statTarget_1.8.0.tar.gz |
| StartedAt: 2018-04-12 10:03:59 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 10:05:14 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 75.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: statTarget.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings statTarget_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/statTarget.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.8.0’ * 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 loading without being on the library search path ... 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 ... 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 installed files from ‘inst/doc’ ... 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: OK
statTarget.Rcheck/00install.out
* installing *source* package ‘statTarget’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (statTarget)
statTarget.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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://github.com/13479776/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")
Data File Checking Start..., Time: Thu Apr 12 10:05:08 2018
172 Pheno Samples vs 172 Profile samples
The Pheno 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"
Phenotype 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
statTarget: shiftCor start...Time: Thu Apr 12 10:05:08 2018
Step 1: Evaluation of missing value...
The number of NA value in Data Profile before QC-RLSC: 336
The number of variables including 80 % of missing value : 0
Step 2: Imputation start...
The number of NA value in Data Profile after the initial imputation: 0
Imputation Finished!
Step 3: QC-RLSC Start... Time: Thu Apr 12 10:05:08 2018
Warning: The QCspan was set at 0.75
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High-resolution images output...
Calculation of CV distribution of raw peaks (QC)...
CV<5% CV<10% CV<15% CV<20% CV<25% CV<30% CV<35%
Batch_1 4.166667 43.75000 64.58333 75.00000 83.33333 91.66667 93.75000
Batch_2 18.750000 64.58333 79.16667 83.33333 93.75000 95.83333 95.83333
Batch_3 10.416667 43.75000 75.00000 81.25000 85.41667 91.66667 95.83333
Batch_4 6.250000 60.41667 75.00000 79.16667 91.66667 91.66667 93.75000
Total 0.000000 16.66667 35.41667 66.66667 68.75000 77.08333 79.16667
CV<40% CV<45% CV<50% CV<55% CV<60% CV<65% CV<70% CV<75%
Batch_1 95.83333 97.91667 100.00000 100.00000 100.00000 100 100 100
Batch_2 95.83333 95.83333 97.91667 97.91667 97.91667 100 100 100
Batch_3 97.91667 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 79.16667 85.41667 89.58333 95.83333 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 4.166667 43.75000 68.75000 77.08333 89.58333 91.66667 95.83333
Batch_2 16.666667 54.16667 72.91667 83.33333 93.75000 95.83333 95.83333
Batch_3 4.166667 31.25000 68.75000 77.08333 81.25000 89.58333 95.83333
Batch_4 0.000000 39.58333 58.33333 70.83333 85.41667 93.75000 97.91667
Total 0.000000 33.33333 60.41667 81.25000 87.50000 95.83333 95.83333
CV<40% CV<45% CV<50% CV<55% CV<60% CV<65% CV<70% CV<75%
Batch_1 95.83333 100.00000 100.00000 100.00000 100.00000 100 100 100
Batch_2 95.83333 95.83333 97.91667 97.91667 97.91667 100 100 100
Batch_3 97.91667 97.91667 97.91667 100.00000 100.00000 100 100 100
Batch_4 100.00000 100.00000 100.00000 100.00000 100.00000 100 100 100
Total 97.91667 100.00000 100.00000 100.00000 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
Correction Finished! Time: Thu Apr 12 10:05:10 2018There were 48 warnings (use warnings() to see them)
>
> #test_check("statTarget")
>
> proc.time()
user system elapsed
3.695 0.178 3.913
statTarget.Rcheck/statTarget-Ex.timings
| name | user | system | elapsed | |
| shiftCor | 1.978 | 0.071 | 2.071 | |
| statAnalysis | 4.358 | 0.056 | 4.462 | |
| statTargetGUI | 0.000 | 0.000 | 0.001 | |
| transCode | 0.012 | 0.001 | 0.016 | |
| transX | 0.039 | 0.002 | 0.043 | |