Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:05:47 -0400 (Fri, 30 Jul 2021).

CHECK results for bnem on tokay2

To the developers/maintainers of the bnem package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bnem.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 204/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bnem 1.0.0  (landing page)
Martin Pirkl
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/bnem
Branch: RELEASE_3_13
Last Commit: 3109efd
Last Changed Date: 2021-05-19 12:58:21 -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    NA    OK    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bnem
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bnem.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bnem_1.0.0.tar.gz
StartedAt: 2021-07-29 20:42:26 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 20:47:28 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 301.6 seconds
RetCode: 0
Status:   OK  
CheckDir: bnem.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bnem.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bnem_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/bnem.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bnem/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bnem' version '1.0.0'
* 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 'bnem' 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: 'rmarkdown'
  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
** running examples for arch 'x64' ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/bnem.Rcheck/00check.log'
for details.



Installation output

bnem.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/bnem_1.0.0.tar.gz && rm -rf bnem.buildbin-libdir && mkdir bnem.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bnem.buildbin-libdir bnem_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL bnem_1.0.0.zip && rm bnem_1.0.0.tar.gz bnem_1.0.0.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  631k   35  224k    0     0  1088k      0 --:--:-- --:--:-- --:--:-- 1088k
100  631k  100  631k    0     0  1933k      0 --:--:-- --:--:-- --:--:-- 1930k

install for i386

* installing *source* package 'bnem' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bnem'
    finding HTML links ... done
    absorption                              html  
    absorptionII                            html  
    addNoise                                html  
    bcr                                     html  
    bnem                                    html  
    bnemBs                                  html  
    computeFc                               html  
    convertGraph                            html  
    dummyCNOlist                            html  
    epiNEM2Bg                               html  
    findResiduals                           html  
    plot.bnem                               html  
    plot.bnembs                             html  
    plot.bnemsim                            html  
    processDataBCR                          html  
    randomDnf                               html  
    reduceGraph                             html  
    scoreDnf                                html  
    simBoolGtn                              html  
    simulateStatesRecursive                 html  
    transClose                              html  
    transRed                                html  
    validateGraph                           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 'bnem' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bnem' as bnem_1.0.0.zip
* DONE (bnem)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'bnem' successfully unpacked and MD5 sums checked

Tests output

bnem.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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("bnem")


RUNIT TEST PROTOCOL -- Thu Jul 29 20:47:07 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bnem RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.50    0.65   10.14 

bnem.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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("bnem")


RUNIT TEST PROTOCOL -- Thu Jul 29 20:47:18 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bnem RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.73    0.56   10.28 

Example timings

bnem.Rcheck/examples_i386/bnem-Ex.timings

nameusersystemelapsed
absorption000
absorptionII000
addNoise1.270.111.39
bcr0.010.000.01
bnem0.10.00.1
bnemBs0.460.040.50
computeFc0.020.000.01
convertGraph000
dummyCNOlist0.020.000.02
epiNEM2Bg0.090.000.22
findResiduals0.280.040.32
plot.bnem0.590.190.78
plot.bnembs0.520.050.57
plot.bnemsim0.190.000.18
processDataBCR000
randomDnf000
reduceGraph000
scoreDnf0.050.000.05
simBoolGtn0.090.000.09
simulateStatesRecursive0.020.000.02
transClose0.020.000.01
transRed0.010.000.02
validateGraph0.130.000.12

bnem.Rcheck/examples_x64/bnem-Ex.timings

nameusersystemelapsed
absorption000
absorptionII000
addNoise1.310.031.36
bcr0.020.000.01
bnem0.060.020.08
bnemBs0.580.030.61
computeFc000
convertGraph000
dummyCNOlist0.000.010.02
epiNEM2Bg0.110.000.14
findResiduals0.290.020.31
plot.bnem0.910.030.94
plot.bnembs0.840.000.84
plot.bnemsim0.250.000.25
processDataBCR0.020.000.02
randomDnf000
reduceGraph0.010.000.01
scoreDnf0.040.000.03
simBoolGtn0.100.000.11
simulateStatesRecursive0.020.000.02
transClose0.020.000.01
transRed0.020.000.01
validateGraph0.150.000.16