Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:02 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biosigner on tokay2


To the developers/maintainers of the biosigner package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biosigner.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 192/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.22.0  (landing page)
Philippe Rinaudo , Etienne Thevenot
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/biosigner
git_branch: RELEASE_3_14
git_last_commit: 72d39bd
git_last_commit_date: 2021-10-26 12:25:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biosigner
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biosigner_1.22.0.tar.gz
StartedAt: 2022-01-20 16:43:27 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 16:48:58 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 331.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biosigner.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosigner.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biosigner_1.22.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/biosigner.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.22.0'
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
biosign 44.67   0.81   45.81
plot    34.74   0.03   34.76
getMset 32.35   0.16   32.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
biosign 46.61   0.29   46.89
plot    38.71   0.00   38.71
getMset 33.14   0.08   33.22
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/biosigner.Rcheck/00check.log'
for details.



Installation output

biosigner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biosigner_1.22.0.tar.gz && rm -rf biosigner.buildbin-libdir && mkdir biosigner.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biosigner.buildbin-libdir biosigner_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biosigner_1.22.0.zip && rm biosigner_1.22.0.tar.gz biosigner_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 81 3106k   81 2535k    0     0  3140k      0 --:--:-- --:--:-- --:--:-- 3141k
100 3106k  100 3106k    0     0  3378k      0 --:--:-- --:--:-- --:--:-- 3377k

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_1.22.0.zip
* DONE (biosigner)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'biosigner' successfully unpacked and MD5 sums checked

Tests output


Example timings

biosigner.Rcheck/examples_i386/biosigner-Ex.timings

nameusersystemelapsed
biosign-class2.970.093.07
biosign44.67 0.8145.81
biosignMultiDataSet-class000
biosigner-package2.950.022.97
getAccuracyMN2.560.002.56
getEset2.610.032.64
getMset32.35 0.1632.50
getSignatureLs3.510.033.55
plot34.74 0.0334.76
predict2.900.022.93
show2.490.002.48

biosigner.Rcheck/examples_x64/biosigner-Ex.timings

nameusersystemelapsed
biosign-class2.890.062.95
biosign46.61 0.2946.89
biosignMultiDataSet-class000
biosigner-package3.220.013.24
getAccuracyMN2.810.002.89
getEset3.000.023.01
getMset33.14 0.0833.22
getSignatureLs2.620.002.63
plot38.71 0.0038.71
predict3.150.023.17
show2.600.002.59