Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:05:07 -0400 (Mon, 20 Sep 2021).

CHECK results for BioMM on tokay2

To the developers/maintainers of the BioMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioMM.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 182/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMM 1.8.0  (landing page)
Junfang Chen
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/BioMM
git_branch: RELEASE_3_13
git_last_commit: 765ffb7
git_last_commit_date: 2021-05-19 12:41:03 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: BioMM
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioMM_1.8.0.tar.gz
StartedAt: 2021-09-19 19:33:39 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 19:45:39 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 719.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioMM_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioMM.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioMM' version '1.8.0'
* package encoding: UTF-8
* 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 'BioMM' 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
Namespaces in Imports field not imported from:
  'imager' 'topGO' 'xlsx'
  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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getDataByFilter     193.28   0.57  193.84
reconByUnsupervised  25.30   0.03   25.33
predByBS             19.81   1.16   21.14
reconBySupervised     6.22   0.08    6.30
getMetrics            2.79   0.18   12.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getDataByFilter     234.04   0.69  235.72
reconByUnsupervised  37.50   0.08   37.58
predByBS             19.49   0.90   18.63
reconBySupervised     7.61   0.00    7.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTest.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTest.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioMM.Rcheck/00check.log'
for details.



Installation output

BioMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BioMM_1.8.0.tar.gz && rm -rf BioMM.buildbin-libdir && mkdir BioMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioMM.buildbin-libdir BioMM_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BioMM_1.8.0.zip && rm BioMM_1.8.0.tar.gz BioMM_1.8.0.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
 35 2551k   35  916k    0     0  2434k      0  0:00:01 --:--:--  0:00:01 2436k
100 2551k  100 2551k    0     0  4230k      0 --:--:-- --:--:-- --:--:-- 4231k

install for i386

* installing *source* package 'BioMM' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioMM'
    finding HTML links ... done
    BioMM                                   html  
    BioMMstage2pred                         html  
    baseGLMnet                              html  
    baseModel                               html  
    baseRandForest                          html  
    baseSVM                                 html  
    cirPlot4pathway                         html  
    classifiACC                             html  
    getDataByFilter                         html  
    getMetrics                              html  
    omics2pathlist                          html  
    plotRankedFeature                       html  
    plotVarExplained                        html  
    predByBS                                html  
    predByCV                                html  
    predByFS                                html  
    reconBySupervised                       html  
    reconByUnsupervised                     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 'BioMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioMM' as BioMM_1.8.0.zip
* DONE (BioMM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BioMM' successfully unpacked and MD5 sums checked

Tests output

BioMM.Rcheck/tests_i386/runTest.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("BioMM")


RUNIT TEST PROTOCOL -- Sun Sep 19 19:45:26 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BioMM RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.00    0.40    4.39 

BioMM.Rcheck/tests_x64/runTest.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("BioMM")


RUNIT TEST PROTOCOL -- Sun Sep 19 19:45:31 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BioMM RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   3.92    0.28    4.14 

Example timings

BioMM.Rcheck/examples_i386/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.550.030.75
baseGLMnet0.650.030.69
baseModel0.510.010.47
baseRandForest0.540.070.56
baseSVM1.310.031.34
classifiACC2.110.152.17
getDataByFilter193.28 0.57193.84
getMetrics 2.79 0.1812.71
omics2pathlist0.500.030.54
predByBS19.81 1.1621.14
predByCV4.550.174.59
predByFS2.290.052.29
reconBySupervised6.220.086.30
reconByUnsupervised25.30 0.0325.33

BioMM.Rcheck/examples_x64/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.310.010.32
baseGLMnet0.390.060.45
baseModel0.420.004.45
baseRandForest0.560.010.58
baseSVM1.430.041.45
classifiACC2.420.123.11
getDataByFilter234.04 0.69235.72
getMetrics1.880.192.39
omics2pathlist0.390.000.39
predByBS19.49 0.9018.63
predByCV4.500.254.65
predByFS3.870.023.90
reconBySupervised7.610.007.60
reconByUnsupervised37.50 0.0837.58