Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:31 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 BiRewire on machv2


To the developers/maintainers of the BiRewire package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiRewire.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 197/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.26.0  (landing page)
Andrea Gobbi
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: RELEASE_3_14
git_last_commit: 0c583a5
git_last_commit_date: 2021-10-26 12:09:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    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: BiRewire
Version: 3.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiRewire_3.26.0.tar.gz
StartedAt: 2022-01-13 10:42:48 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:47:31 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 283.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiRewire_3.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiRewire.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiRewire’ 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
* 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 ... OK
* checking R code for possible problems ... NOTE
birewire.analysis.bipartite: no visible binding for global variable
  ‘sd’
birewire.analysis.bipartite: no visible global function definition for
  ‘qt’
birewire.analysis.bipartite: no visible global function definition for
  ‘par’
birewire.analysis.bipartite: no visible global function definition for
  ‘polygon’
birewire.analysis.bipartite: no visible global function definition for
  ‘lines’
birewire.analysis.bipartite: no visible global function definition for
  ‘abline’
birewire.analysis.bipartite: no visible global function definition for
  ‘legend’
birewire.analysis.dsg: no visible global function definition for
  ‘dev.off’
birewire.analysis.dsg: no visible binding for global variable ‘sd’
birewire.analysis.dsg: no visible global function definition for ‘qt’
birewire.analysis.dsg: no visible global function definition for
  ‘polygon’
birewire.analysis.dsg: no visible global function definition for
  ‘lines’
birewire.analysis.dsg: no visible global function definition for
  ‘abline’
birewire.analysis.dsg: no visible global function definition for
  ‘legend’
birewire.analysis.undirected: no visible binding for global variable
  ‘sd’
birewire.analysis.undirected: no visible global function definition for
  ‘qt’
birewire.analysis.undirected: no visible global function definition for
  ‘par’
birewire.analysis.undirected: no visible global function definition for
  ‘polygon’
birewire.analysis.undirected: no visible global function definition for
  ‘lines’
birewire.analysis.undirected: no visible global function definition for
  ‘abline’
birewire.analysis.undirected: no visible global function definition for
  ‘legend’
birewire.load.dsg: no visible global function definition for
  ‘read.table’
birewire.sampler.bipartite: no visible global function definition for
  ‘write.table’
birewire.sampler.undirected: no visible global function definition for
  ‘write.table’
birewire.save.dsg: no visible global function definition for
  ‘write.table’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘par’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘colorRampPalette’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘text’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘par’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘colorRampPalette’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘text’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘par’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘colorRampPalette’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘text’
Undefined global functions or variables:
  abline colorRampPalette dev.off legend lines par polygon qt
  read.table sd text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "polygon",
             "text")
  importFrom("stats", "qt", "sd")
  importFrom("utils", "read.table", "write.table")
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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          75.267  0.192  75.534
birewire.visual.monitoring.dsg        66.194  0.329  66.578
birewire.visual.monitoring.undirected 18.402  0.426  18.841
birewire.visual.monitoring.bipartite  10.153  0.091  10.249
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interface.c -o interface.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-BiRewire/00new/BiRewire/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiRewire)

Tests output

BiRewire.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> require(BiRewire) || stop("unable to load MyPackage")
Loading required package: BiRewire
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: slam
Loading required package: tsne
Loading required package: Matrix
[1] TRUE
> BiocGenerics:::testPackage('BiRewire')
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[1] "You are using a matrix with NA. It is strongly suggested to use MAXITER_MUL=100 and exact=TRUE because the number of configuration with the NA constrain can terribly decrease, the routine will use  these."
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[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 21.599575949753
Epoch: Iteration #200 error is: 0.541413142499769
Epoch: Iteration #300 error is: 0.295834534427675
Epoch: Iteration #400 error is: 0.270245543162281
Epoch: Iteration #500 error is: 0.256495007274405
Epoch: Iteration #600 error is: 0.253257325342581
Epoch: Iteration #700 error is: 0.252593360213614
Epoch: Iteration #800 error is: 0.252206090460972
Epoch: Iteration #900 error is: 0.251755110576416
Epoch: Iteration #1000 error is: 0.251285712250051
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.0630294286943
Epoch: Iteration #200 error is: 0.635279555491772
Epoch: Iteration #300 error is: 0.330975384509912
Epoch: Iteration #400 error is: 0.294260087300548
Epoch: Iteration #500 error is: 0.280532667902929
Epoch: Iteration #600 error is: 0.265719719927064
Epoch: Iteration #700 error is: 0.256496237652629
Epoch: Iteration #800 error is: 0.253808980621497
Epoch: Iteration #900 error is: 0.253249435220224
Epoch: Iteration #1000 error is: 0.25297830512162
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.6045423616572
Epoch: Iteration #200 error is: 0.491562719458519
Epoch: Iteration #300 error is: 0.299787915820073
Epoch: Iteration #400 error is: 0.276214804083383
Epoch: Iteration #500 error is: 0.256530075848579
Epoch: Iteration #600 error is: 0.253322277573274
Epoch: Iteration #700 error is: 0.252157316504669
Epoch: Iteration #800 error is: 0.251455347260168
Epoch: Iteration #900 error is: 0.251014702579045
Epoch: Iteration #1000 error is: 0.250866220164506
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.7561452781338
Epoch: Iteration #200 error is: 0.284948671061374
Epoch: Iteration #300 error is: 0.252014445234133
Epoch: Iteration #400 error is: 0.251937430600367
Epoch: Iteration #500 error is: 0.251936343844897
Epoch: Iteration #600 error is: 0.251936211574216
Epoch: Iteration #700 error is: 0.251936209372147
Epoch: Iteration #800 error is: 0.251936209258323
Epoch: Iteration #900 error is: 0.251936209108939
Epoch: Iteration #1000 error is: 0.251936208911817
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 26.2372348996205
Epoch: Iteration #200 error is: 0.864721339823111
Epoch: Iteration #300 error is: 0.534786479536257
Epoch: Iteration #400 error is: 0.392533758314755
Epoch: Iteration #500 error is: 0.289812595401751
Epoch: Iteration #600 error is: 0.268429582321855
Epoch: Iteration #700 error is: 0.263301488957134
Epoch: Iteration #800 error is: 0.258596291366131
Epoch: Iteration #900 error is: 0.254645895639676
Epoch: Iteration #1000 error is: 0.253016036091625
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.668075317802
Epoch: Iteration #200 error is: 0.655107665182774
Epoch: Iteration #300 error is: 0.36282148782733
Epoch: Iteration #400 error is: 0.302430958235153
Epoch: Iteration #500 error is: 0.278024606347837
Epoch: Iteration #600 error is: 0.271284053113733
Epoch: Iteration #700 error is: 0.263069900533084
Epoch: Iteration #800 error is: 0.254565196875188
Epoch: Iteration #900 error is: 0.252368886528755
Epoch: Iteration #1000 error is: 0.252085488929239
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.013098735469
Epoch: Iteration #200 error is: 0.253278352008326
Epoch: Iteration #300 error is: 0.250920787461182
Epoch: Iteration #400 error is: 0.250824623753736
Epoch: Iteration #500 error is: 0.250824199560797
Epoch: Iteration #600 error is: 0.250823629712159
Epoch: Iteration #700 error is: 0.250823131322981
Epoch: Iteration #800 error is: 0.25082283592819
Epoch: Iteration #900 error is: 0.250822710573408
Epoch: Iteration #1000 error is: 0.25082266641132
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 21.1978239299067
Epoch: Iteration #200 error is: 0.354724383756737
Epoch: Iteration #300 error is: 0.255719546196923
Epoch: Iteration #400 error is: 0.251988637871839
Epoch: Iteration #500 error is: 0.251943054810455
Epoch: Iteration #600 error is: 0.251937503428832
Epoch: Iteration #700 error is: 0.251937019376654
Epoch: Iteration #800 error is: 0.251937006457432
Epoch: Iteration #900 error is: 0.251937006318043
Epoch: Iteration #1000 error is: 0.251937006289418


RUNIT TEST PROTOCOL -- Thu Jan 13 10:47:22 2022 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiRewire RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
2: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
3: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
4: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
5: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
6: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
7: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
8: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
> 
> proc.time()
   user  system elapsed 
 29.121   2.687  31.995 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1490.3920.544
birewire.analysis.dsg0.0510.0100.061
birewire.analysis.undirected75.267 0.19275.534
birewire.bipartite.from.incidence0.0120.0510.063
birewire.build.dsg0.0110.0030.014
birewire.induced.bipartite0.0050.0020.006
birewire.rewire.bipartite0.0080.0350.044
birewire.rewire.bipartite.and.projections0.1420.0150.156
birewire.rewire.dsg0.0060.0020.009
birewire.rewire.undirected1.0570.0761.134
birewire.similarity0.0130.0010.014
birewire.similarity.dsg0.0360.0040.039
birewire.visual.monitoring.bipartite10.153 0.09110.249
birewire.visual.monitoring.dsg66.194 0.32966.578
birewire.visual.monitoring.undirected18.402 0.42618.841