Package: biosigner

Version: 1.8.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings biosigner_1.8.0.tar.gz

StartedAt: 2018-10-15 22:49:37 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 22:50:33 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 55.5 seconds

RetCode: 0

Status:  OK

CheckDir: biosigner.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings biosigner_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/biosigner.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ 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 ‘biosigner’ 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL biosigner
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘biosigner’ ...
** R
** data
** 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
* DONE (biosigner)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("biosigner")
Significant features from 'S' groups:
              plsda randomforest svm
m427.215t07.9 "A"   "S"          "B"
m189.040t01.2 "S"   "A"          "E"
Accuracy:
     plsda randomforest   svm
Full 0.723        0.702 0.746
AS   0.696        0.797 0.514
S    0.762        0.715    NA
Significant features from 'S' groups:
              plsda
m189.040t01.2 "S"  
Accuracy:
     plsda
Full 0.723
AS   0.762
S    0.737
Significant features from 'S' groups:
              plsda randomforest svm
m427.215t07.9 "A"   "S"          "A"
m646.309t07.8 "A"   "C"          "S"
m497.117t07.7 "S"   "A"          "D"
m164.035t02.1 "A"   "E"          "S"
m189.040t01.2 "E"   "S"          "B"
m557.311t10.9 "S"   "E"          "C"
m607.308t10.0 "S"   "E"          "C"
m481.313t10.6 "S"   "E"          "D"
m096.009t01.6 "E"   "E"          "S"
m203.083t05.3 "E"   "E"          "S"
Accuracy:
     plsda randomforest   svm
Full 0.633        0.533 0.929
AS   0.838        0.789 0.612
S    0.742        0.854 0.479
Significant features from 'S' groups:
              randomforest
m189.040t01.2 "S"         
m427.215t07.9 "S"         
Accuracy:
     randomforest
Full        0.679
AS          0.739
S           0.698
Significant features from 'S' groups:
                               plsda randomforest svm
Oxoglutaric acid               "S"   "S"          "S"
p-Anisic acid                  "S"   "S"          "S"
Testosterone glucuronide       "S"   "S"          "S"
Acetylphenylalanine            "S"   "A"          "S"
Malic acid                     "S"   "A"          "S"
Pantothenic acid               "S"   "B"          "S"
Gluconic acid and/or isomers   "S"   "E"          "C"
Taurine                        "C"   "E"          "S"
N4-Acetylcytidine              "D"   "E"          "S"
alpha-N-Phenylacetyl-glutamine "S"   "E"          "E"
Citric acid                    "S"   "E"          "E"
Glucuronic acid and/or isomers "S"   "E"          "E"
Hippuric acid                  "S"   "E"          "E"
Monoethyl phthalate            "E"   "E"          "S"
Phe-Tyr-Asp (and isomers)      "S"   "E"          "E"
Threonic acid/Erythronic acid  "S"   "E"          "E"
Accuracy:
     plsda randomforest   svm
Full 0.896        0.893 0.897
AS   0.862        0.879 0.910
S    0.869        0.869 0.896
No significant variable found for the selected classifier(s): 'svm'


RUNIT TEST PROTOCOL -- Mon Oct 15 22:50:31 2018 
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Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
biosigner RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
There were 23 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 13.196   0.044  13.291 

name	user	system	elapsed
biosign-class	2.552	0.012	2.587
biosign	2.516	0.004	2.521
biosigner-package	2.184	0.004	2.192
getAccuracyMN	2.200	0.004	2.210
getSignatureLs	2.128	0.000	2.131
plot	2.092	0.008	2.103
predict	2.104	0.004	2.108
show	2.244	0.000	2.246