Package: BiRewire

Version: 3.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiRewire_3.10.0.tar.gz

StartedAt: 2018-04-12 01:01:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:04:52 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 207.7 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 --no-vignettes --timings BiRewire_3.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiRewire.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘3.10.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          61.000  0.142  62.506
birewire.visual.monitoring.dsg        41.277  0.239  42.222
birewire.visual.monitoring.undirected 13.676  0.816  14.669
birewire.visual.monitoring.bipartite   6.650  0.036   6.808
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

* installing *source* package ‘BiRewire’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -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 /Users/biocbuild/bbs-3.6-bioc/meat/BiRewire.Rcheck/BiRewire/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiRewire)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 9.75214919288898
Epoch: Iteration #200 error is: 0.360559667946118
Epoch: Iteration #300 error is: 0.255787884201431
Epoch: Iteration #400 error is: 0.252128841941616
Epoch: Iteration #500 error is: 0.252006667424709
Epoch: Iteration #600 error is: 0.251949239997246
Epoch: Iteration #700 error is: 0.25193798989705
Epoch: Iteration #800 error is: 0.251937185312318
Epoch: Iteration #900 error is: 0.251937163290345
Epoch: Iteration #1000 error is: 0.251937163040342
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.50374375392971
Epoch: Iteration #200 error is: 0.355477201028694
Epoch: Iteration #300 error is: 0.260294738321064
Epoch: Iteration #400 error is: 0.252968350851044
Epoch: Iteration #500 error is: 0.252267279566954
Epoch: Iteration #600 error is: 0.252107890512314
Epoch: Iteration #700 error is: 0.251989204352074
Epoch: Iteration #800 error is: 0.251944906638016
Epoch: Iteration #900 error is: 0.251938073735365
Epoch: Iteration #1000 error is: 0.251937544092769
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.217472508484
Epoch: Iteration #200 error is: 0.312881129852166
Epoch: Iteration #300 error is: 0.265056824076229
Epoch: Iteration #400 error is: 0.253062117740617
Epoch: Iteration #500 error is: 0.251910328674569
Epoch: Iteration #600 error is: 0.251106880661839
Epoch: Iteration #700 error is: 0.25084919903576
Epoch: Iteration #800 error is: 0.250829141666947
Epoch: Iteration #900 error is: 0.250828445784865
Epoch: Iteration #1000 error is: 0.250828427704618
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.1800127401864
Epoch: Iteration #200 error is: 0.424717060832071
Epoch: Iteration #300 error is: 0.307447760963729
Epoch: Iteration #400 error is: 0.260025349352699
Epoch: Iteration #500 error is: 0.251948674415553
Epoch: Iteration #600 error is: 0.251285533441831
Epoch: Iteration #700 error is: 0.251043015436864
Epoch: Iteration #800 error is: 0.250905735248727
Epoch: Iteration #900 error is: 0.25085163213103
Epoch: Iteration #1000 error is: 0.250836927518511
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 23.8945946086464
Epoch: Iteration #200 error is: 0.91474659507718
Epoch: Iteration #300 error is: 0.422511158076371
Epoch: Iteration #400 error is: 0.306252048838607
Epoch: Iteration #500 error is: 0.277992856698763
Epoch: Iteration #600 error is: 0.270846030162871
Epoch: Iteration #700 error is: 0.267793473132152
Epoch: Iteration #800 error is: 0.26391323489407
Epoch: Iteration #900 error is: 0.257949282915593
Epoch: Iteration #1000 error is: 0.253878614052226
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.3552938482272
Epoch: Iteration #200 error is: 0.318417606322523
Epoch: Iteration #300 error is: 0.26107011300685
Epoch: Iteration #400 error is: 0.252119577271159
Epoch: Iteration #500 error is: 0.25193747903742
Epoch: Iteration #600 error is: 0.251936994993215
Epoch: Iteration #700 error is: 0.251936993871176
Epoch: Iteration #800 error is: 0.251936993767639
Epoch: Iteration #900 error is: 0.251936993734144
Epoch: Iteration #1000 error is: 0.251936993702367
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.81594790345483
Epoch: Iteration #200 error is: 0.2847573076811
Epoch: Iteration #300 error is: 0.253014216858461
Epoch: Iteration #400 error is: 0.252190079466098
Epoch: Iteration #500 error is: 0.250856915524416
Epoch: Iteration #600 error is: 0.250829193123745
Epoch: Iteration #700 error is: 0.25082894571557
Epoch: Iteration #800 error is: 0.2508285916663
Epoch: Iteration #900 error is: 0.250828147185848
Epoch: Iteration #1000 error is: 0.250827674500266
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.7182735448141
Epoch: Iteration #200 error is: 0.741881722908473
Epoch: Iteration #300 error is: 0.363392548473448
Epoch: Iteration #400 error is: 0.27278195665033
Epoch: Iteration #500 error is: 0.264088151213303
Epoch: Iteration #600 error is: 0.253571611444512
Epoch: Iteration #700 error is: 0.251422358833299
Epoch: Iteration #800 error is: 0.251086435882705
Epoch: Iteration #900 error is: 0.25091498046429
Epoch: Iteration #1000 error is: 0.250849883258619


RUNIT TEST PROTOCOL -- Thu Apr 12 01:04:48 2018 
*********************************************** 
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 
 21.596   1.105  23.011 

name	user	system	elapsed
birewire.analysis.bipartite	0.222	0.131	0.362
birewire.analysis.dsg	0.045	0.006	0.052
birewire.analysis.undirected	61.000	0.142	62.506
birewire.bipartite.from.incidence	0.028	0.013	0.041
birewire.build.dsg	0.104	0.005	0.113
birewire.induced.bipartite	0.004	0.001	0.005
birewire.rewire.bipartite	0.054	0.012	0.069
birewire.rewire.bipartite.and.projections	0.174	0.012	0.186
birewire.rewire.dsg	0.005	0.001	0.006
birewire.rewire.undirected	1.044	0.043	1.095
birewire.similarity	0.067	0.001	0.068
birewire.similarity.dsg	0.327	0.010	0.341
birewire.visual.monitoring.bipartite	6.650	0.036	6.808
birewire.visual.monitoring.dsg	41.277	0.239	42.222
birewire.visual.monitoring.undirected	13.676	0.816	14.669