Philippe Rinaudo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/biosigner |
| Branch: RELEASE_3_6 |
| Last Commit: d7dbd40 |
| Last Changed Date: 2017-10-30 12:41:13 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:37 -0400 (Thu, 12 Apr 2018).
| Package 141/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biosigner 1.6.0 Philippe Rinaudo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: biosigner |
| Version: 1.6.0 |
| Command: rm -rf biosigner.buildbin-libdir biosigner.Rcheck && mkdir biosigner.buildbin-libdir biosigner.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biosigner.buildbin-libdir biosigner_1.6.0.tar.gz >biosigner.Rcheck\00install.out 2>&1 && cp biosigner.Rcheck\00install.out biosigner-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biosigner.buildbin-libdir --install="check:biosigner-install.out" --force-multiarch --no-vignettes --timings biosigner_1.6.0.tar.gz |
| StartedAt: 2018-04-11 22:32:30 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:34:38 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 127.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biosigner.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf biosigner.buildbin-libdir biosigner.Rcheck && mkdir biosigner.buildbin-libdir biosigner.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biosigner.buildbin-libdir biosigner_1.6.0.tar.gz >biosigner.Rcheck\00install.out 2>&1 && cp biosigner.Rcheck\00install.out biosigner-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biosigner.buildbin-libdir --install="check:biosigner-install.out" --force-multiarch --no-vignettes --timings biosigner_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/biosigner.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biosign-class 5.25 0.03 5.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
biosigner.Rcheck/00install.out
install for i386
* installing *source* package 'biosigner' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'biosigner'
finding HTML links ... done
biosign-class html
biosign html
biosigner-package html
diaplasma html
getAccuracyMN html
getSignatureLs html
plot html
predict html
show html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'biosigner' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biosigner' as biosigner_1.6.0.zip
* DONE (biosigner)
In R CMD INSTALL
In R CMD INSTALL
|
biosigner.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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" "A"
m189.040t01.2 "S" "S" "E"
m995.613t10.2 "E" "S" "B"
Accuracy:
plsda randomforest svm
Full 0.723 0.701 0.735
AS 0.765 0.829 0.648
S 0.739 0.784 NA
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
m557.311t10.9 "S" "S" "B"
m164.035t02.1 "A" "C" "S"
m497.117t07.7 "S" "C" "A"
m481.313t10.6 "S" "B" "D"
m995.613t10.2 "E" "A" "S"
m203.083t05.3 "E" "B" "S"
m607.308t10.0 "S" "B" "E"
m455.221t08.1 "E" "C" "S"
m511.313t08.7 "E" "C" "S"
m189.040t01.2 "E" "S" "E"
m212.054t03.6 "E" "E" "S"
Accuracy:
plsda randomforest svm
Full 0.633 0.589 0.804
AS 0.938 0.688 0.955
S 0.646 0.583 0.679
Significant features from 'S' groups:
randomforest
m189.040t01.2 "S"
m427.215t07.9 "S"
Accuracy:
randomforest
Full 0.770
AS 0.762
S 0.680
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" "S" "C"
Pantothenic acid "S" "A" "D"
Malic acid "S" "B" "E"
alpha-N-Phenylacetyl-glutamine "S" "E" "E"
Citric acid "S" "E" "E"
Gluconic acid and/or isomers "S" "E" "E"
Glucuronic acid and/or isomers "S" "E" "E"
Hippuric acid "S" "E" "E"
Phe-Tyr-Asp (and isomers) "S" "E" "E"
Threonic acid/Erythronic acid "S" "E" "E"
Accuracy:
plsda randomforest svm
Full 0.896 0.883 0.886
AS 0.877 0.890 0.861
S 0.866 0.893 0.884
dev.new(): using pdf(file="Rplots6.pdf")
No significant variable found for the selected classifier(s): 'svm'
RUNIT TEST PROTOCOL -- Wed Apr 11 22:34:15 2018
***********************************************
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
18.59 0.31 19.04
|
biosigner.Rcheck/tests_x64/runTests.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-w64-mingw32/x64 (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
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
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
dev.new(): using pdf(file="Rplots6.pdf")
No significant variable found for the selected classifier(s): 'svm'
RUNIT TEST PROTOCOL -- Wed Apr 11 22:34:34 2018
***********************************************
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
17.90 0.35 18.32
|
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biosigner.Rcheck/examples_i386/biosigner-Ex.timings
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biosigner.Rcheck/examples_x64/biosigner-Ex.timings
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