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CHECK report for biosigner on tokay1

This page was generated on 2020-08-07 12:08:43 -0400 (Fri, 07 Aug 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 176/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.17.0
Philippe Rinaudo , Etienne Thevenot
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/biosigner
Branch: master
Last Commit: a227d42
Last Changed Date: 2020-04-27 14:55:12 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biosigner
Version: 1.17.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biosigner_1.17.0.tar.gz
StartedAt: 2020-08-07 02:41:29 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 02:48:16 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 407.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biosigner.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biosigner_1.17.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biosigner.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.17.0'
* 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 53.66   0.92   54.58
getMset 44.61   0.32   44.95
plot    36.15   0.00   36.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
biosign 65.61   0.47   66.07
plot    56.55   0.01   56.58
getMset 45.13   0.02   45.15
* 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-3.12-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://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/biosigner_1.17.0.tar.gz && rm -rf biosigner.buildbin-libdir && mkdir biosigner.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biosigner.buildbin-libdir biosigner_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biosigner_1.17.0.zip && rm biosigner_1.17.0.tar.gz biosigner_1.17.0.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
 41 3110k   41 1280k    0     0  1236k      0  0:00:02  0:00:01  0:00:01 1241k
100 3110k  100 3110k    0     0  2543k      0  0:00:01  0:00:01 --:--:-- 2552k

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_1.17.0.zip
* DONE (biosigner)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biosigner' successfully unpacked and MD5 sums checked

Tests output


Example timings

biosigner.Rcheck/examples_i386/biosigner-Ex.timings

nameusersystemelapsed
biosign-class4.770.034.79
biosign53.66 0.9254.58
biosignMultiDataSet-class000
biosigner-package2.920.022.94
getAccuracyMN3.280.013.29
getEset3.270.033.30
getMset44.61 0.3244.95
getSignatureLs3.80.03.8
plot36.15 0.0036.16
predict2.710.002.70
show2.780.002.78

biosigner.Rcheck/examples_x64/biosigner-Ex.timings

nameusersystemelapsed
biosign-class3.900.094.00
biosign65.61 0.4766.07
biosignMultiDataSet-class000
biosigner-package3.510.023.53
getAccuracyMN3.360.003.36
getEset3.060.033.09
getMset45.13 0.0245.15
getSignatureLs4.470.004.46
plot56.55 0.0156.58
predict3.150.023.17
show4.280.004.35