Multiple platform build/check report for BioC 3.6 - CHECK report for biosigner on veracruz1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biosigner_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/biosigner.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 ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.6.0’
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
biosign-class 5.351  0.079    5.53
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  FAILURE in test_biosign_sacurine: Error in checkIdentical(getSignatureLs(biosignLs), sigLs) : FALSE 
   
  
  Test files with failing tests
  
     test_biosigner.R 
       test_biosign_diaplasma 
       test_biosign_predict 
       test_biosign_randomforest 
       test_biosign_sacurine 
  
  
  Error in BiocGenerics:::testPackage("biosigner") : 
    unit tests failed for package biosigner
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/biosigner.Rcheck/00check.log’
for details.


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)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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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
Timing stopped at: 5.971 0.082 6.223
Error in checkIdentical(getSignatureLs(biosignLs), sigLs) : FALSE 
 
In addition: There were 11 warnings (use warnings() to see them)
Significant features from 'S' groups:
              plsda
m189.040t01.2 "S"  
Accuracy:
     plsda
Full 0.723
AS   0.762
S    0.737
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
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
Timing stopped at: 0.789 0.011 0.849
Error in checkEquals(predDIA043Vc, c("T2", "T1")) : 
  Lengths (3, 2) differ (string compare on first 2)

In addition: There were 12 warnings (use warnings() to see them)
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
Timing stopped at: 1.451 0.03 1.586
Error in checkEqualsNumeric(biosignLs@accuracyMN["AS", "randomforest"],  : 
  Mean relative difference: 0.08183474

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
dev.new(): using pdf(file="Rplots6.pdf")
Timing stopped at: 8.626 0.222 9.703
Error in checkIdentical(getSignatureLs(biosignLs), sigLs) : FALSE 
 
No significant variable found for the selected classifier(s): 'svm'


RUNIT TEST PROTOCOL -- Thu Apr 12 01:00:53 2018 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 4 

 
1 Test Suite : 
biosigner RUnit Tests - 6 test functions, 0 errors, 4 failures
FAILURE in test_biosign_diaplasma: Error in checkIdentical(getSignatureLs(biosignLs), sigLs) : FALSE 
 
FAILURE in test_biosign_predict: Error in checkEquals(predDIA043Vc, c("T2", "T1")) : 
  Lengths (3, 2) differ (string compare on first 2)

FAILURE in test_biosign_randomforest: Error in checkEqualsNumeric(biosignLs@accuracyMN["AS", "randomforest"],  : 
  Mean relative difference: 0.08183474

FAILURE in test_biosign_sacurine: Error in checkIdentical(getSignatureLs(biosignLs), sigLs) : FALSE 
 

Test files with failing tests

   test_biosigner.R 
     test_biosign_diaplasma 
     test_biosign_predict 
     test_biosign_randomforest 
     test_biosign_sacurine 


Error in BiocGenerics:::testPackage("biosigner") : 
  unit tests failed for package biosigner
Execution halted

name	user	system	elapsed
biosign-class	5.351	0.079	5.530
biosign	3.092	0.060	3.231
biosigner-package	2.367	0.045	2.440
getAccuracyMN	2.664	0.034	2.739
getSignatureLs	2.581	0.042	2.679
plot	2.713	0.045	2.796
predict	2.593	0.042	2.683
show	2.590	0.049	2.708

CHECK report for biosigner on veracruz1

Summary

Command output

Installation output

Tests output

Example timings