Package: BiRewire

Version: 3.16.0

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_3.16.0.tar.gz

StartedAt: 2019-10-16 01:00:07 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:05:16 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 308.1 seconds

RetCode: 0

Status:  OK

CheckDir: BiRewire.Rcheck

Warnings: 0

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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_3.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiRewire.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.16.0’
* 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
  ‘plot’
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 ‘plot’
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
  ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 plot polygon qt
  read.table sd text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "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 or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          83.421  0.281  83.716
birewire.visual.monitoring.dsg        67.695  1.184  68.906
birewire.visual.monitoring.undirected 20.410  2.303  22.717
birewire.visual.monitoring.bipartite  10.386  0.158  10.546
* 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-3.9-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiRewire
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c interface.c -o interface.o
clang -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/3.6/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 14.7953231957343
Epoch: Iteration #200 error is: 1.07281233540925
Epoch: Iteration #300 error is: 0.422161615307669
Epoch: Iteration #400 error is: 0.287735838106735
Epoch: Iteration #500 error is: 0.276763811476006
Epoch: Iteration #600 error is: 0.271651275919106
Epoch: Iteration #700 error is: 0.26415967123378
Epoch: Iteration #800 error is: 0.254694308327617
Epoch: Iteration #900 error is: 0.25211930122952
Epoch: Iteration #1000 error is: 0.251794583611987
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.9391360766826
Epoch: Iteration #200 error is: 0.318504210341078
Epoch: Iteration #300 error is: 0.269184405041249
Epoch: Iteration #400 error is: 0.254768320011952
Epoch: Iteration #500 error is: 0.253393607907835
Epoch: Iteration #600 error is: 0.252673276948007
Epoch: Iteration #700 error is: 0.252568305272106
Epoch: Iteration #800 error is: 0.252385598455515
Epoch: Iteration #900 error is: 0.252025999556186
Epoch: Iteration #1000 error is: 0.251938958703824
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.069705397662
Epoch: Iteration #200 error is: 0.379388673358055
Epoch: Iteration #300 error is: 0.258307984753735
Epoch: Iteration #400 error is: 0.25202893135827
Epoch: Iteration #500 error is: 0.251937849626005
Epoch: Iteration #600 error is: 0.251937265269089
Epoch: Iteration #700 error is: 0.251937259716003
Epoch: Iteration #800 error is: 0.251937258364899
Epoch: Iteration #900 error is: 0.251937258182307
Epoch: Iteration #1000 error is: 0.251937258160939
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.3938967433385
Epoch: Iteration #200 error is: 0.285489388490316
Epoch: Iteration #300 error is: 0.252405627585602
Epoch: Iteration #400 error is: 0.251953798971259
Epoch: Iteration #500 error is: 0.251938267962831
Epoch: Iteration #600 error is: 0.25193653374316
Epoch: Iteration #700 error is: 0.251936462608497
Epoch: Iteration #800 error is: 0.251936462042731
Epoch: Iteration #900 error is: 0.251936461961763
Epoch: Iteration #1000 error is: 0.251936461852006
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.45436587019766
Epoch: Iteration #200 error is: 0.474734125377438
Epoch: Iteration #300 error is: 0.316993991550351
Epoch: Iteration #400 error is: 0.277656743339351
Epoch: Iteration #500 error is: 0.267443435279746
Epoch: Iteration #600 error is: 0.257275397444261
Epoch: Iteration #700 error is: 0.253397802143826
Epoch: Iteration #800 error is: 0.252041487897481
Epoch: Iteration #900 error is: 0.251947599738234
Epoch: Iteration #1000 error is: 0.251938846691195
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.0752317993714
Epoch: Iteration #200 error is: 0.319419857450695
Epoch: Iteration #300 error is: 0.273881757071962
Epoch: Iteration #400 error is: 0.259827262694732
Epoch: Iteration #500 error is: 0.255982880132484
Epoch: Iteration #600 error is: 0.25468155854983
Epoch: Iteration #700 error is: 0.253538966328653
Epoch: Iteration #800 error is: 0.252121013045157
Epoch: Iteration #900 error is: 0.251027536732457
Epoch: Iteration #1000 error is: 0.250837794481151
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.81046688415603
Epoch: Iteration #200 error is: 0.264775226031365
Epoch: Iteration #300 error is: 0.252561689272573
Epoch: Iteration #400 error is: 0.252249490346071
Epoch: Iteration #500 error is: 0.251942120258469
Epoch: Iteration #600 error is: 0.251935920446143
Epoch: Iteration #700 error is: 0.251935914508442
Epoch: Iteration #800 error is: 0.251935914367895
Epoch: Iteration #900 error is: 0.251935914159469
Epoch: Iteration #1000 error is: 0.25193591388003
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.7516851031238
Epoch: Iteration #200 error is: 0.723042226362869
Epoch: Iteration #300 error is: 0.345372473751232
Epoch: Iteration #400 error is: 0.271883765606284
Epoch: Iteration #500 error is: 0.2566922780904
Epoch: Iteration #600 error is: 0.253147782811923
Epoch: Iteration #700 error is: 0.252460304299854
Epoch: Iteration #800 error is: 0.252345935089009
Epoch: Iteration #900 error is: 0.252254221680449
Epoch: Iteration #1000 error is: 0.25214169117228


RUNIT TEST PROTOCOL -- Wed Oct 16 01:05:08 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
 31.996   3.438  35.388 

name	user	system	elapsed
birewire.analysis.bipartite	0.283	0.409	0.695
birewire.analysis.dsg	0.076	0.027	0.103
birewire.analysis.undirected	83.421	0.281	83.716
birewire.bipartite.from.incidence	0.016	0.026	0.041
birewire.build.dsg	0.009	0.001	0.011
birewire.induced.bipartite	0.005	0.001	0.007
birewire.rewire.bipartite	0.017	0.030	0.047
birewire.rewire.bipartite.and.projections	0.153	0.021	0.174
birewire.rewire.dsg	0.008	0.003	0.010
birewire.rewire.undirected	1.618	0.117	1.735
birewire.similarity	0.015	0.001	0.016
birewire.similarity.dsg	0.041	0.004	0.045
birewire.visual.monitoring.bipartite	10.386	0.158	10.546
birewire.visual.monitoring.dsg	67.695	1.184	68.906
birewire.visual.monitoring.undirected	20.410	2.303	22.717