Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-21 15:05:20 -0400 (Wed, 21 Jul 2021).

CHECK results for epiNEM on tokay2

To the developers/maintainers of the epiNEM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiNEM.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 585/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epiNEM 1.16.0  (landing page)
Martin Pirkl
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/epiNEM
Branch: RELEASE_3_13
Last Commit: 2383f66
Last Changed Date: 2021-05-19 12:26:21 -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    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: epiNEM
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epiNEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epiNEM_1.16.0.tar.gz
StartedAt: 2021-07-20 23:35:11 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 23:39:16 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 244.8 seconds
RetCode: 0
Status:   OK  
CheckDir: epiNEM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epiNEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epiNEM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/epiNEM.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 'epiNEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epiNEM' version '1.16.0'
* 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 'epiNEM' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("getTruthTable_R", ..., PACKAGE = "BoolNet")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
SimEpiNEM: no visible global function definition for 'epiNEM2Bg'
SimEpiNEM: no visible global function definition for 'dummyCNOlist'
SimEpiNEM: no visible global function definition for 'readSIF'
SimEpiNEM: no visible global function definition for 'preprocessing'
SimEpiNEM: no visible global function definition for 'absorption'
SimEpiNEM: no visible global function definition for 'bnem'
SimEpiNEM: no visible binding for global variable 'popSize'
SimEpiNEM: no visible global function definition for 'computeFc'
SimEpiNEM: no visible global function definition for
  'simulateStatesRecursive'
SimEpiNEM: no visible global function definition for 'dnf2adj'
epiNEM: no visible binding for global variable 'inference'
plot.epiSim: no visible binding for global variable 'sim'
plot.epiSim: no visible global function definition for 'layout'
plot.epiSim: no visible global function definition for 'boxplot'
plot.epiSim: no visible global function definition for 'abline'
plot.epiSim: no visible global function definition for 'axis'
Undefined global functions or variables:
  abline absorption axis bnem boxplot computeFc dnf2adj dummyCNOlist
  epiNEM2Bg inference layout popSize preprocessing readSIF sim
  simulateStatesRecursive
Consider adding
  importFrom("graphics", "abline", "axis", "boxplot", "layout")
to your NAMESPACE file.
* 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 LazyData ... 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
plot.epiScreen 9.39   0.02    9.41
epiScreen      8.92   0.00    8.92
plot.epiSim    6.61   0.01    6.62
SimEpiNEM      6.39   0.07    6.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
epiScreen      10.60   0.00   10.59
plot.epiScreen 10.50   0.00   10.50
plot.epiSim     6.89   0.00    6.89
SimEpiNEM       6.54   0.07    6.61
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/epiNEM.Rcheck/00check.log'
for details.



Installation output

epiNEM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/epiNEM_1.16.0.tar.gz && rm -rf epiNEM.buildbin-libdir && mkdir epiNEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epiNEM.buildbin-libdir epiNEM_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL epiNEM_1.16.0.zip && rm epiNEM_1.16.0.tar.gz epiNEM_1.16.0.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
 21  196k   21 43227    0     0   403k      0 --:--:-- --:--:-- --:--:--  402k
100  196k  100  196k    0     0  1270k      0 --:--:-- --:--:-- --:--:-- 1268k

install for i386

* installing *source* package 'epiNEM' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epiNEM'
    finding HTML links ... done
    AddLogicGates                           html  
    CreateExtendedAdjacency                 html  
    CreateRandomGraph                       html  
    CreateTopology                          html  
    ExtendTopology                          html  
    GenerateData                            html  
    HeatmapOP                               html  
    Mll                                     html  
    SimEpiNEM                               html  
    epiAnno                                 html  
    epiNEM                                  html  
    epiScreen                               html  
    perm.rank.test                          html  
    plot.epiNEM                             html  
    plot.epiScreen                          html  
    plot.epiSim                             html  
    rank.enrichment                         html  
    sameith_GO                              html  
    sameith_string                          html  
    samscreen                               html  
    sim                                     html  
    wageningen_GO                           html  
    wageningen_string                       html  
    wagscreen                               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 'epiNEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epiNEM' as epiNEM_1.16.0.zip
* DONE (epiNEM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'epiNEM' successfully unpacked and MD5 sums checked

Tests output

epiNEM.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("epiNEM")
[1] "Progress (of 1 iterations):"

1...


RUNIT TEST PROTOCOL -- Tue Jul 20 23:39:00 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epiNEM 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 
   6.50    0.50    6.98 

epiNEM.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("epiNEM")
[1] "Progress (of 1 iterations):"

1...


RUNIT TEST PROTOCOL -- Tue Jul 20 23:39:08 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epiNEM 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 
   6.57    0.37    6.93 

Example timings

epiNEM.Rcheck/examples_i386/epiNEM-Ex.timings

nameusersystemelapsed
AddLogicGates000
CreateExtendedAdjacency0.110.000.16
CreateRandomGraph000
CreateTopology0.090.000.09
ExtendTopology0.080.000.08
GenerateData0.080.020.09
HeatmapOP0.120.050.17
Mll0.020.000.02
SimEpiNEM6.390.076.47
epiAnno0.20.00.2
epiNEM0.850.000.85
epiScreen8.920.008.92
perm.rank.test0.330.020.34
plot.epiNEM0.710.000.72
plot.epiScreen9.390.029.41
plot.epiSim6.610.016.62
rank.enrichment0.320.030.35
sameith_GO000
sameith_string000
samscreen0.000.020.01
sim000
wageningen_GO000
wageningen_string000
wagscreen0.000.010.02

epiNEM.Rcheck/examples_x64/epiNEM-Ex.timings

nameusersystemelapsed
AddLogicGates000
CreateExtendedAdjacency0.090.000.09
CreateRandomGraph000
CreateTopology0.080.000.08
ExtendTopology0.060.000.06
GenerateData0.360.000.36
HeatmapOP0.110.000.11
Mll000
SimEpiNEM6.540.076.61
epiAnno0.190.000.19
epiNEM0.870.000.88
epiScreen10.60 0.0010.59
perm.rank.test0.390.020.41
plot.epiNEM0.890.000.89
plot.epiScreen10.5 0.010.5
plot.epiSim6.890.006.89
rank.enrichment0.300.010.31
sameith_GO000
sameith_string000
samscreen000
sim0.000.020.02
wageningen_GO000
wageningen_string000
wagscreen000