Martin Pirkl
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/epiNEM |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2383f66 |
| git_last_commit_date: 2021-05-19 12:26:21 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
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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. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 585/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epiNEM 1.16.0 (landing page) Martin Pirkl
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2021-10-14 22:50:01 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:54:04 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 243.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epiNEM.Rcheck |
| Warnings: 0 |
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### Running command:
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### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/epiNEM.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 '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 9.41 0.01 9.42
epiScreen 8.72 0.00 8.72
SimEpiNEM 6.24 0.16 6.41
plot.epiSim 6.15 0.00 6.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
epiScreen 11.12 0.01 11.15
plot.epiScreen 10.89 0.02 10.91
SimEpiNEM 7.14 0.13 7.26
plot.epiSim 7.26 0.00 7.26
* 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.
epiNEM.Rcheck/00install.out
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###
### 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
###
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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
100 196k 100 196k 0 0 721k 0 --:--:-- --:--:-- --:--:-- 723k
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
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epiNEM.Rcheck/tests_i386/runTests.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("epiNEM")
[1] "Progress (of 1 iterations):"
1...
RUNIT TEST PROTOCOL -- Thu Oct 14 22:53:50 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
5.87 0.40 6.25
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epiNEM.Rcheck/tests_x64/runTests.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("epiNEM")
[1] "Progress (of 1 iterations):"
1...
RUNIT TEST PROTOCOL -- Thu Oct 14 22:53:57 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
6.29 0.42 6.70
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epiNEM.Rcheck/examples_i386/epiNEM-Ex.timings
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epiNEM.Rcheck/examples_x64/epiNEM-Ex.timings
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