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CHECK report for biosigner on tokay2

This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biosigner PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 181/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.16.0
Philippe Rinaudo , Etienne Thevenot
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/biosigner
Branch: RELEASE_3_11
Last Commit: 7ffb4ea
Last Changed Date: 2020-04-27 14:55:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biosigner
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biosigner_1.16.0.tar.gz
StartedAt: 2020-10-17 02:00:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:06:51 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 374.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biosigner.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biosigner_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biosigner.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.16.0'
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'MultiDataSet'
  All declared Imports should be used.
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'getMset,biosignMultiDataSet-method':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
biosign 49.24   0.96   50.31
plot    37.20   0.02   37.22
getMset 32.72   0.03   32.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
biosign 50.86   0.33   51.29
plot    46.75   0.06   46.81
getMset 46.30   0.02   46.37
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/biosigner.Rcheck/00check.log'
for details.



Installation output

biosigner.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/biosigner_1.16.0.tar.gz && rm -rf biosigner.buildbin-libdir && mkdir biosigner.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biosigner.buildbin-libdir biosigner_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL biosigner_1.16.0.zip && rm biosigner_1.16.0.tar.gz biosigner_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3110k  100 3110k    0     0  28.5M      0 --:--:-- --:--:-- --:--:-- 30.0M

install for i386

* installing *source* package 'biosigner' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'biosign' with signature 'x="MultiDataSet"': no definition for class "MultiDataSet"
** help
*** installing help indices
  converting help for package 'biosigner'
    finding HTML links ... done
    biosign-class                           html  
    biosign                                 html  
    biosignMultiDataSet-class               html  
    biosigner-package                       html  
    diaplasma                               html  
    getAccuracyMN                           html  
    getEset                                 html  
    getMset                                 html  
    getSignatureLs                          html  
    plot                                    html  
    predict                                 html  
    show                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'biosigner' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biosigner' as biosigner_1.16.0.zip
* DONE (biosigner)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'biosigner' successfully unpacked and MD5 sums checked

Tests output


Example timings

biosigner.Rcheck/examples_i386/biosigner-Ex.timings

nameusersystemelapsed
biosign-class3.390.043.44
biosign49.24 0.9650.31
biosignMultiDataSet-class000
biosigner-package2.720.022.74
getAccuracyMN2.670.012.69
getEset3.120.023.14
getMset32.72 0.0332.75
getSignatureLs2.750.002.75
plot37.20 0.0237.22
predict2.940.002.93
show2.700.002.71

biosigner.Rcheck/examples_x64/biosigner-Ex.timings

nameusersystemelapsed
biosign-class3.310.073.38
biosign50.86 0.3351.29
biosignMultiDataSet-class000
biosigner-package2.980.003.03
getAccuracyMN3.410.003.41
getEset3.620.013.67
getMset46.30 0.0246.37
getSignatureLs3.640.013.66
plot46.75 0.0646.81
predict3.480.003.49
show4.440.024.45