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CHECK report for BiRewire on merida1

This page was generated on 2020-08-10 12:34:57 -0400 (Mon, 10 Aug 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 181/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.21.0
Andrea Gobbi
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: master
Last Commit: 7ab05ed
Last Changed Date: 2020-04-27 14:36:26 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.21.0
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_3.21.0.tar.gz
StartedAt: 2020-08-10 00:08:44 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 00:12:58 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 254.3 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_3.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiRewire.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘3.21.0’
* 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          63.955  0.199  64.227
birewire.visual.monitoring.dsg        62.116  0.328  62.524
birewire.visual.monitoring.undirected 17.056  0.354  17.431
birewire.visual.monitoring.bipartite   9.720  0.088   9.817
* 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-3.12-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
###
##############################################################################
##############################################################################


* 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 4.0.2 (2020-06-22) -- "Taking Off Again"
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: 13.8014284353203
Epoch: Iteration #200 error is: 0.92223201767462
Epoch: Iteration #300 error is: 0.384631136720069
Epoch: Iteration #400 error is: 0.298268679441807
Epoch: Iteration #500 error is: 0.273687308678479
Epoch: Iteration #600 error is: 0.262832867665893
Epoch: Iteration #700 error is: 0.260296267948191
Epoch: Iteration #800 error is: 0.258543391978825
Epoch: Iteration #900 error is: 0.256527180366039
Epoch: Iteration #1000 error is: 0.254616905843628
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.60654034378046
Epoch: Iteration #200 error is: 0.372263270113935
Epoch: Iteration #300 error is: 0.263509916727352
Epoch: Iteration #400 error is: 0.252730656799661
Epoch: Iteration #500 error is: 0.251983247990442
Epoch: Iteration #600 error is: 0.251937939035076
Epoch: Iteration #700 error is: 0.251937260460251
Epoch: Iteration #800 error is: 0.251937138802107
Epoch: Iteration #900 error is: 0.251937127787469
Epoch: Iteration #1000 error is: 0.251937127419457
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 17.7189048894769
Epoch: Iteration #200 error is: 0.266330931312403
Epoch: Iteration #300 error is: 0.254195481860095
Epoch: Iteration #400 error is: 0.250938879179678
Epoch: Iteration #500 error is: 0.250829999282995
Epoch: Iteration #600 error is: 0.250829986878656
Epoch: Iteration #700 error is: 0.250829966716828
Epoch: Iteration #800 error is: 0.250829923987048
Epoch: Iteration #900 error is: 0.25082983217567
Epoch: Iteration #1000 error is: 0.250829624576419
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.6849758165318
Epoch: Iteration #200 error is: 0.283452582742786
Epoch: Iteration #300 error is: 0.26224450146999
Epoch: Iteration #400 error is: 0.258438983595045
Epoch: Iteration #500 error is: 0.25250660393487
Epoch: Iteration #600 error is: 0.25083882152999
Epoch: Iteration #700 error is: 0.250827327931854
Epoch: Iteration #800 error is: 0.250827309892131
Epoch: Iteration #900 error is: 0.250827291899487
Epoch: Iteration #1000 error is: 0.250827272313869
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.7511481792118
Epoch: Iteration #200 error is: 0.271639520903106
Epoch: Iteration #300 error is: 0.253729589459022
Epoch: Iteration #400 error is: 0.252009366600376
Epoch: Iteration #500 error is: 0.25193614705903
Epoch: Iteration #600 error is: 0.251936011885199
Epoch: Iteration #700 error is: 0.251936005321343
Epoch: Iteration #800 error is: 0.251936005181828
Epoch: Iteration #900 error is: 0.251936005027347
Epoch: Iteration #1000 error is: 0.251936004810402
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 27.1633986127142
Epoch: Iteration #200 error is: 0.606225454849119
Epoch: Iteration #300 error is: 0.371703047079888
Epoch: Iteration #400 error is: 0.292220353038605
Epoch: Iteration #500 error is: 0.272805938983991
Epoch: Iteration #600 error is: 0.261514766865914
Epoch: Iteration #700 error is: 0.254029006342543
Epoch: Iteration #800 error is: 0.25224878107487
Epoch: Iteration #900 error is: 0.251838888320996
Epoch: Iteration #1000 error is: 0.251568525812715
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.2208525508241
Epoch: Iteration #200 error is: 0.540006522124519
Epoch: Iteration #300 error is: 0.354438951455132
Epoch: Iteration #400 error is: 0.310356556945717
Epoch: Iteration #500 error is: 0.272743941163083
Epoch: Iteration #600 error is: 0.258239407250056
Epoch: Iteration #700 error is: 0.25549733828278
Epoch: Iteration #800 error is: 0.254512324989147
Epoch: Iteration #900 error is: 0.253768262912565
Epoch: Iteration #1000 error is: 0.252993282190478
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.9972134278676
Epoch: Iteration #200 error is: 0.628325797262695
Epoch: Iteration #300 error is: 0.331252269680641
Epoch: Iteration #400 error is: 0.275541823236692
Epoch: Iteration #500 error is: 0.260269943148455
Epoch: Iteration #600 error is: 0.256261385184437
Epoch: Iteration #700 error is: 0.255122773522904
Epoch: Iteration #800 error is: 0.254253518447664
Epoch: Iteration #900 error is: 0.253431151641366
Epoch: Iteration #1000 error is: 0.252535749795059


RUNIT TEST PROTOCOL -- Mon Aug 10 00:12:49 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 
 26.475   2.376  28.975 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1400.3420.483
birewire.analysis.dsg0.0520.0100.062
birewire.analysis.undirected63.955 0.19964.227
birewire.bipartite.from.incidence0.0110.0410.052
birewire.build.dsg0.0100.0020.012
birewire.induced.bipartite0.0040.0020.006
birewire.rewire.bipartite0.0100.0400.049
birewire.rewire.bipartite.and.projections0.1280.0180.147
birewire.rewire.dsg0.0060.0020.009
birewire.rewire.undirected0.8230.0600.883
birewire.similarity0.0130.0010.014
birewire.similarity.dsg0.1670.0080.176
birewire.visual.monitoring.bipartite9.7200.0889.817
birewire.visual.monitoring.dsg62.116 0.32862.524
birewire.visual.monitoring.undirected17.056 0.35417.431