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CHECK report for BiRewire on machv2

This page was generated on 2020-10-17 11:58:08 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiRewire PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 187/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.20.0
Andrea Gobbi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_11
Last Commit: 6b3b1f2
Last Changed Date: 2020-04-27 14:36:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.20.0.tar.gz
StartedAt: 2020-10-16 23:09:47 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:14:28 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 281.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiRewire.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘3.20.0’
* 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          73.347  0.223  73.671
birewire.visual.monitoring.dsg        67.831  0.390  68.297
birewire.visual.monitoring.undirected 18.283  0.424  18.734
birewire.visual.monitoring.bipartite  10.589  0.094  10.691
* 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-3.11-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 12.3491057240232
Epoch: Iteration #200 error is: 0.639900337491756
Epoch: Iteration #300 error is: 0.361443326977947
Epoch: Iteration #400 error is: 0.298555313856849
Epoch: Iteration #500 error is: 0.272856832222482
Epoch: Iteration #600 error is: 0.263232992163215
Epoch: Iteration #700 error is: 0.258223627302762
Epoch: Iteration #800 error is: 0.254482179933518
Epoch: Iteration #900 error is: 0.25260621507154
Epoch: Iteration #1000 error is: 0.25206646333342
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.8211594189852
Epoch: Iteration #200 error is: 0.336595577181804
Epoch: Iteration #300 error is: 0.267112597708876
Epoch: Iteration #400 error is: 0.253401557781613
Epoch: Iteration #500 error is: 0.252047194651973
Epoch: Iteration #600 error is: 0.251973488609767
Epoch: Iteration #700 error is: 0.251942668315491
Epoch: Iteration #800 error is: 0.251937627309287
Epoch: Iteration #900 error is: 0.251937317396788
Epoch: Iteration #1000 error is: 0.25193730939791
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.7593452856214
Epoch: Iteration #200 error is: 0.629790039069155
Epoch: Iteration #300 error is: 0.304323916533342
Epoch: Iteration #400 error is: 0.265579966129857
Epoch: Iteration #500 error is: 0.254850730047046
Epoch: Iteration #600 error is: 0.252372888364364
Epoch: Iteration #700 error is: 0.251877493935712
Epoch: Iteration #800 error is: 0.251361115739329
Epoch: Iteration #900 error is: 0.250983242318094
Epoch: Iteration #1000 error is: 0.250853637699107
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.4721970936506
Epoch: Iteration #200 error is: 0.278574830615449
Epoch: Iteration #300 error is: 0.252331099716998
Epoch: Iteration #400 error is: 0.251939500480088
Epoch: Iteration #500 error is: 0.251936449007082
Epoch: Iteration #600 error is: 0.251936155948569
Epoch: Iteration #700 error is: 0.251936150209381
Epoch: Iteration #800 error is: 0.251936150077151
Epoch: Iteration #900 error is: 0.251936149917479
Epoch: Iteration #1000 error is: 0.251936149705086
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.07031973471647
Epoch: Iteration #200 error is: 0.324977563699156
Epoch: Iteration #300 error is: 0.2699264271005
Epoch: Iteration #400 error is: 0.264548666451
Epoch: Iteration #500 error is: 0.255675054770505
Epoch: Iteration #600 error is: 0.252784639747329
Epoch: Iteration #700 error is: 0.250913777507382
Epoch: Iteration #800 error is: 0.250833477641645
Epoch: Iteration #900 error is: 0.250833243559848
Epoch: Iteration #1000 error is: 0.250833242567488
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.0114334295223
Epoch: Iteration #200 error is: 0.307028816456408
Epoch: Iteration #300 error is: 0.266727854408426
Epoch: Iteration #400 error is: 0.256110910485888
Epoch: Iteration #500 error is: 0.253208073932948
Epoch: Iteration #600 error is: 0.251579976547978
Epoch: Iteration #700 error is: 0.250882878159705
Epoch: Iteration #800 error is: 0.250832686042422
Epoch: Iteration #900 error is: 0.250831631621647
Epoch: Iteration #1000 error is: 0.250831537681968
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.1686130005559
Epoch: Iteration #200 error is: 0.261214560036443
Epoch: Iteration #300 error is: 0.251936060313636
Epoch: Iteration #400 error is: 0.251935522414503
Epoch: Iteration #500 error is: 0.25193551872248
Epoch: Iteration #600 error is: 0.251935518210455
Epoch: Iteration #700 error is: 0.251935517982958
Epoch: Iteration #800 error is: 0.251935517648555
Epoch: Iteration #900 error is: 0.251935517201058
Epoch: Iteration #1000 error is: 0.251935516642956
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.88870415458443
Epoch: Iteration #200 error is: 0.252481635553544
Epoch: Iteration #300 error is: 0.250820733973808
Epoch: Iteration #400 error is: 0.250820687577118
Epoch: Iteration #500 error is: 0.250820622524679
Epoch: Iteration #600 error is: 0.250820551961659
Epoch: Iteration #700 error is: 0.250820501445466
Epoch: Iteration #800 error is: 0.250820470879214
Epoch: Iteration #900 error is: 0.250820450272716
Epoch: Iteration #1000 error is: 0.250820431022302


RUNIT TEST PROTOCOL -- Fri Oct 16 23:14:19 2020 
*********************************************** 
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 
 29.904   2.588  32.600 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1610.4720.641
birewire.analysis.dsg0.0610.0140.075
birewire.analysis.undirected73.347 0.22373.671
birewire.bipartite.from.incidence0.0140.0470.060
birewire.build.dsg0.0140.0020.016
birewire.induced.bipartite0.0050.0020.007
birewire.rewire.bipartite0.0070.0240.031
birewire.rewire.bipartite.and.projections0.1380.0190.157
birewire.rewire.dsg0.0060.0030.009
birewire.rewire.undirected0.9770.0781.055
birewire.similarity0.0080.0010.009
birewire.similarity.dsg0.1860.0120.197
birewire.visual.monitoring.bipartite10.589 0.09410.691
birewire.visual.monitoring.dsg67.831 0.39068.297
birewire.visual.monitoring.undirected18.283 0.42418.734