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CHECK report for statTarget on veracruz1

This page was generated on 2018-04-12 13:43:45 -0400 (Thu, 12 Apr 2018).

Package 1359/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
statTarget 1.8.0
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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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###
### 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


Installation output

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)

Tests output

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 

Example timings

statTarget.Rcheck/statTarget-Ex.timings

nameusersystemelapsed
shiftCor1.9780.0712.071
statAnalysis4.3580.0564.462
statTargetGUI0.0000.0000.001
transCode0.0120.0010.016
transX0.0390.0020.043