Package: BiRewire

Version: 3.15.0

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_3.15.0.tar.gz

StartedAt: 2019-04-09 00:16:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:20:59 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 293.2 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_3.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiRewire.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘3.15.0’
* 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          80.364  0.233  80.599
birewire.visual.monitoring.dsg        62.186  1.270  63.464
birewire.visual.monitoring.undirected 22.496  2.553  25.054
birewire.visual.monitoring.bipartite   9.182  0.141   9.323
* 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   -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 /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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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: 17.9536749918273
Epoch: Iteration #200 error is: 1.20218691253908
Epoch: Iteration #300 error is: 0.557710580171399
Epoch: Iteration #400 error is: 0.337443337637096
Epoch: Iteration #500 error is: 0.300477698897709
Epoch: Iteration #600 error is: 0.273515570915005
Epoch: Iteration #700 error is: 0.257998402001785
Epoch: Iteration #800 error is: 0.253496055156571
Epoch: Iteration #900 error is: 0.252415713008998
Epoch: Iteration #1000 error is: 0.252100480374604
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.92257750228249
Epoch: Iteration #200 error is: 0.259695513931226
Epoch: Iteration #300 error is: 0.253014731728632
Epoch: Iteration #400 error is: 0.250835118270035
Epoch: Iteration #500 error is: 0.25082678482888
Epoch: Iteration #600 error is: 0.250826782060327
Epoch: Iteration #700 error is: 0.250826778609262
Epoch: Iteration #800 error is: 0.250826774799155
Epoch: Iteration #900 error is: 0.250826771269821
Epoch: Iteration #1000 error is: 0.250826768358882
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.6772438859676
Epoch: Iteration #200 error is: 0.70443674015072
Epoch: Iteration #300 error is: 0.350397089259877
Epoch: Iteration #400 error is: 0.293606212533413
Epoch: Iteration #500 error is: 0.277239088305632
Epoch: Iteration #600 error is: 0.270573970660438
Epoch: Iteration #700 error is: 0.268349862871655
Epoch: Iteration #800 error is: 0.26681465379362
Epoch: Iteration #900 error is: 0.264832648596484
Epoch: Iteration #1000 error is: 0.26206043829238
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.76413025844348
Epoch: Iteration #200 error is: 0.271779318281523
Epoch: Iteration #300 error is: 0.252074999556847
Epoch: Iteration #400 error is: 0.250967936381713
Epoch: Iteration #500 error is: 0.250830517993606
Epoch: Iteration #600 error is: 0.250830168105794
Epoch: Iteration #700 error is: 0.250829957907946
Epoch: Iteration #800 error is: 0.250829637753468
Epoch: Iteration #900 error is: 0.250829209434554
Epoch: Iteration #1000 error is: 0.25082869791846
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.423982446969
Epoch: Iteration #200 error is: 0.755288422435679
Epoch: Iteration #300 error is: 0.378496597633439
Epoch: Iteration #400 error is: 0.273348133543189
Epoch: Iteration #500 error is: 0.257805834841839
Epoch: Iteration #600 error is: 0.252978208698265
Epoch: Iteration #700 error is: 0.252187583396106
Epoch: Iteration #800 error is: 0.252040042070904
Epoch: Iteration #900 error is: 0.25199755703837
Epoch: Iteration #1000 error is: 0.251974802685241
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.73188836455084
Epoch: Iteration #200 error is: 0.334962056384328
Epoch: Iteration #300 error is: 0.256896342395072
Epoch: Iteration #400 error is: 0.252565845519237
Epoch: Iteration #500 error is: 0.250978916757989
Epoch: Iteration #600 error is: 0.250830677554153
Epoch: Iteration #700 error is: 0.250830219658205
Epoch: Iteration #800 error is: 0.250830019341875
Epoch: Iteration #900 error is: 0.250829725557888
Epoch: Iteration #1000 error is: 0.250829347218592
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.5752754784357
Epoch: Iteration #200 error is: 0.286401819178388
Epoch: Iteration #300 error is: 0.266880958515098
Epoch: Iteration #400 error is: 0.253902744997489
Epoch: Iteration #500 error is: 0.251998708729254
Epoch: Iteration #600 error is: 0.251944407703709
Epoch: Iteration #700 error is: 0.251936304491896
Epoch: Iteration #800 error is: 0.251936129801743
Epoch: Iteration #900 error is: 0.251936129304083
Epoch: Iteration #1000 error is: 0.251936129160643
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.7605836116793
Epoch: Iteration #200 error is: 0.400564764094604
Epoch: Iteration #300 error is: 0.283332811598951
Epoch: Iteration #400 error is: 0.256054523589694
Epoch: Iteration #500 error is: 0.252185126987845
Epoch: Iteration #600 error is: 0.251974327613406
Epoch: Iteration #700 error is: 0.251950405399004
Epoch: Iteration #800 error is: 0.251943395402904
Epoch: Iteration #900 error is: 0.251939636648574
Epoch: Iteration #1000 error is: 0.251938208783737


RUNIT TEST PROTOCOL -- Tue Apr  9 00:20:51 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 
 29.470   2.696  32.139 

name	user	system	elapsed
birewire.analysis.bipartite	0.250	0.367	0.627
birewire.analysis.dsg	0.050	0.019	0.069
birewire.analysis.undirected	80.364	0.233	80.599
birewire.bipartite.from.incidence	0.019	0.034	0.053
birewire.build.dsg	0.010	0.002	0.011
birewire.induced.bipartite	0.003	0.001	0.005
birewire.rewire.bipartite	0.017	0.031	0.047
birewire.rewire.bipartite.and.projections	0.137	0.022	0.160
birewire.rewire.dsg	0.007	0.002	0.009
birewire.rewire.undirected	1.347	0.105	1.453
birewire.similarity	0.012	0.001	0.013
birewire.similarity.dsg	0.035	0.004	0.039
birewire.visual.monitoring.bipartite	9.182	0.141	9.323
birewire.visual.monitoring.dsg	62.186	1.270	63.464
birewire.visual.monitoring.undirected	22.496	2.553	25.054