Package: BiRewire

Version: 3.10.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiRewire_3.10.0.tar.gz

StartedAt: 2018-04-11 21:51:37 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:54:33 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 176.3 seconds

RetCode: 0

Status:  OK

CheckDir: BiRewire.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiRewire_3.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BiRewire.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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          61.960  0.052  62.069
birewire.visual.monitoring.dsg        30.020  0.008  30.046
birewire.visual.monitoring.undirected 11.648  0.008  11.662
birewire.visual.monitoring.bipartite   5.100  0.008   5.110
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

* installing *source* package ‘BiRewire’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BiRewire.c -o BiRewire.o
BiRewire.c: In function ‘rewire_sparse’:
BiRewire.c:1066:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) {
                ^
BiRewire.c: In function ‘rewire_sparse_ex’:
BiRewire.c:1149:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) {
                ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/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-pc-linux-gnu (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: 15.0023637639487
Epoch: Iteration #200 error is: 0.253831907944963
Epoch: Iteration #300 error is: 0.250825870047357
Epoch: Iteration #400 error is: 0.250825240734125
Epoch: Iteration #500 error is: 0.250825101536721
Epoch: Iteration #600 error is: 0.250824713082511
Epoch: Iteration #700 error is: 0.250823759099801
Epoch: Iteration #800 error is: 0.250822108153566
Epoch: Iteration #900 error is: 0.250820836839257
Epoch: Iteration #1000 error is: 0.250820449970535
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.2948287759981
Epoch: Iteration #200 error is: 0.790162626943238
Epoch: Iteration #300 error is: 0.323817361375989
Epoch: Iteration #400 error is: 0.265840049026764
Epoch: Iteration #500 error is: 0.253852898116862
Epoch: Iteration #600 error is: 0.252181333959113
Epoch: Iteration #700 error is: 0.25200315182936
Epoch: Iteration #800 error is: 0.251963987378936
Epoch: Iteration #900 error is: 0.251949830978934
Epoch: Iteration #1000 error is: 0.251942972650475
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.2431903174142
Epoch: Iteration #200 error is: 0.506160996119956
Epoch: Iteration #300 error is: 0.363599309513562
Epoch: Iteration #400 error is: 0.316605425573608
Epoch: Iteration #500 error is: 0.289218663334719
Epoch: Iteration #600 error is: 0.271056073577052
Epoch: Iteration #700 error is: 0.263540262601581
Epoch: Iteration #800 error is: 0.258884550092624
Epoch: Iteration #900 error is: 0.255089395807719
Epoch: Iteration #1000 error is: 0.252953234890779
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.67500720198382
Epoch: Iteration #200 error is: 0.346970953512611
Epoch: Iteration #300 error is: 0.266363152350208
Epoch: Iteration #400 error is: 0.256832559841279
Epoch: Iteration #500 error is: 0.255024083546938
Epoch: Iteration #600 error is: 0.25301810687471
Epoch: Iteration #700 error is: 0.251225905060878
Epoch: Iteration #800 error is: 0.250841059894496
Epoch: Iteration #900 error is: 0.250831222362055
Epoch: Iteration #1000 error is: 0.25083105242393
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.2722173205822
Epoch: Iteration #200 error is: 0.271982915911186
Epoch: Iteration #300 error is: 0.252570422098325
Epoch: Iteration #400 error is: 0.251937557795359
Epoch: Iteration #500 error is: 0.251936431433711
Epoch: Iteration #600 error is: 0.251936353197805
Epoch: Iteration #700 error is: 0.251936349750688
Epoch: Iteration #800 error is: 0.251936349656183
Epoch: Iteration #900 error is: 0.251936349553546
Epoch: Iteration #1000 error is: 0.251936349413164
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.19113382110798
Epoch: Iteration #200 error is: 0.335306398767597
Epoch: Iteration #300 error is: 0.27950369565964
Epoch: Iteration #400 error is: 0.271246626187247
Epoch: Iteration #500 error is: 0.264664406915837
Epoch: Iteration #600 error is: 0.254886978283899
Epoch: Iteration #700 error is: 0.252703497382694
Epoch: Iteration #800 error is: 0.252606233850384
Epoch: Iteration #900 error is: 0.252543418660776
Epoch: Iteration #1000 error is: 0.25241145905938
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.8515303768091
Epoch: Iteration #200 error is: 0.268527143559525
Epoch: Iteration #300 error is: 0.252830452951575
Epoch: Iteration #400 error is: 0.251400614678459
Epoch: Iteration #500 error is: 0.250824764995237
Epoch: Iteration #600 error is: 0.250824754517772
Epoch: Iteration #700 error is: 0.250824747928065
Epoch: Iteration #800 error is: 0.250824740435179
Epoch: Iteration #900 error is: 0.25082473376505
Epoch: Iteration #1000 error is: 0.250824728491652
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.8429300804397
Epoch: Iteration #200 error is: 0.508717827081367
Epoch: Iteration #300 error is: 0.293626749548264
Epoch: Iteration #400 error is: 0.271322091418825
Epoch: Iteration #500 error is: 0.268252239365127
Epoch: Iteration #600 error is: 0.2656678945913
Epoch: Iteration #700 error is: 0.26138550610149
Epoch: Iteration #800 error is: 0.255278781409693
Epoch: Iteration #900 error is: 0.252499800217421
Epoch: Iteration #1000 error is: 0.252047666238349


RUNIT TEST PROTOCOL -- Wed Apr 11 21:54:31 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 
 16.856   0.496  17.355 

name	user	system	elapsed
birewire.analysis.bipartite	0.124	0.068	0.192
birewire.analysis.dsg	0.028	0.004	0.034
birewire.analysis.undirected	61.960	0.052	62.069
birewire.bipartite.from.incidence	0.012	0.008	0.022
birewire.build.dsg	0.080	0.000	0.078
birewire.induced.bipartite	0.000	0.004	0.002
birewire.rewire.bipartite	0.040	0.004	0.047
birewire.rewire.bipartite.and.projections	0.124	0.004	0.130
birewire.rewire.dsg	0.004	0.000	0.003
birewire.rewire.undirected	0.824	0.024	0.848
birewire.similarity	0.048	0.000	0.046
birewire.similarity.dsg	0.184	0.000	0.186
birewire.visual.monitoring.bipartite	5.100	0.008	5.110
birewire.visual.monitoring.dsg	30.020	0.008	30.046
birewire.visual.monitoring.undirected	11.648	0.008	11.662