Package: BiRewire

Version: 3.18.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiRewire_3.18.0.tar.gz

StartedAt: 2020-04-15 01:52:00 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:55:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 223.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiRewire.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiRewire_3.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BiRewire.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘3.18.0’
* 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 ... WARNING
Found the following significant warnings:
  BiRewire.c:1066:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  BiRewire.c:1149:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/BiRewire.Rcheck/00install.out’ for details.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          87.912  0.036  88.127
birewire.visual.monitoring.dsg        42.536  0.004  42.633
birewire.visual.monitoring.undirected 14.248  0.056  14.330
birewire.visual.monitoring.bipartite   6.800  0.016   6.826
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BiRewire
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 26.3293623693717
Epoch: Iteration #200 error is: 0.399923634296161
Epoch: Iteration #300 error is: 0.268781608517769
Epoch: Iteration #400 error is: 0.25486542392693
Epoch: Iteration #500 error is: 0.252682309603238
Epoch: Iteration #600 error is: 0.25257874666751
Epoch: Iteration #700 error is: 0.252456629361813
Epoch: Iteration #800 error is: 0.25204705893046
Epoch: Iteration #900 error is: 0.25115106394958
Epoch: Iteration #1000 error is: 0.250842111221458
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.36794582766012
Epoch: Iteration #200 error is: 0.265606910773939
Epoch: Iteration #300 error is: 0.25116755814705
Epoch: Iteration #400 error is: 0.250830560594693
Epoch: Iteration #500 error is: 0.250827093435111
Epoch: Iteration #600 error is: 0.250826970614556
Epoch: Iteration #700 error is: 0.250826803748336
Epoch: Iteration #800 error is: 0.250826625148822
Epoch: Iteration #900 error is: 0.250826466025834
Epoch: Iteration #1000 error is: 0.250826345266914
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.0704041511711
Epoch: Iteration #200 error is: 0.732944717949526
Epoch: Iteration #300 error is: 0.373227138664788
Epoch: Iteration #400 error is: 0.270561823931769
Epoch: Iteration #500 error is: 0.259756317136198
Epoch: Iteration #600 error is: 0.253707046741981
Epoch: Iteration #700 error is: 0.252577730894138
Epoch: Iteration #800 error is: 0.252480374656874
Epoch: Iteration #900 error is: 0.252406939220544
Epoch: Iteration #1000 error is: 0.252302060901019
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.6598538883898
Epoch: Iteration #200 error is: 0.253044430982424
Epoch: Iteration #300 error is: 0.25191574491523
Epoch: Iteration #400 error is: 0.251915659949565
Epoch: Iteration #500 error is: 0.251915496865678
Epoch: Iteration #600 error is: 0.251915255117583
Epoch: Iteration #700 error is: 0.251914936310518
Epoch: Iteration #800 error is: 0.251914525400298
Epoch: Iteration #900 error is: 0.251914016534702
Epoch: Iteration #1000 error is: 0.251913393099246
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.78461679879748
Epoch: Iteration #200 error is: 0.632951583762973
Epoch: Iteration #300 error is: 0.303467971950794
Epoch: Iteration #400 error is: 0.272492273261563
Epoch: Iteration #500 error is: 0.263660080681233
Epoch: Iteration #600 error is: 0.255928577120948
Epoch: Iteration #700 error is: 0.253921024589461
Epoch: Iteration #800 error is: 0.25346523760823
Epoch: Iteration #900 error is: 0.252920549028534
Epoch: Iteration #1000 error is: 0.252214219456911
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.3594612651923
Epoch: Iteration #200 error is: 1.05462903221624
Epoch: Iteration #300 error is: 0.475425545090609
Epoch: Iteration #400 error is: 0.297362570995286
Epoch: Iteration #500 error is: 0.279932901009914
Epoch: Iteration #600 error is: 0.272654246011747
Epoch: Iteration #700 error is: 0.268309729857059
Epoch: Iteration #800 error is: 0.263425751491905
Epoch: Iteration #900 error is: 0.257754597250041
Epoch: Iteration #1000 error is: 0.254515009258613
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.753554755073
Epoch: Iteration #200 error is: 0.698394547148343
Epoch: Iteration #300 error is: 0.322411970025499
Epoch: Iteration #400 error is: 0.272381431027436
Epoch: Iteration #500 error is: 0.262333945397022
Epoch: Iteration #600 error is: 0.259145852680408
Epoch: Iteration #700 error is: 0.25775474677793
Epoch: Iteration #800 error is: 0.25676912904546
Epoch: Iteration #900 error is: 0.255843058654477
Epoch: Iteration #1000 error is: 0.254608391408267
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.7030267151243
Epoch: Iteration #200 error is: 0.309547497163778
Epoch: Iteration #300 error is: 0.255005478961742
Epoch: Iteration #400 error is: 0.252745123229596
Epoch: Iteration #500 error is: 0.251936266999594
Epoch: Iteration #600 error is: 0.251936012349939
Epoch: Iteration #700 error is: 0.251936010099929
Epoch: Iteration #800 error is: 0.251936009908646
Epoch: Iteration #900 error is: 0.251936009746084
Epoch: Iteration #1000 error is: 0.251936009516642


RUNIT TEST PROTOCOL -- Wed Apr 15 01:55:40 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 
> 
> proc.time()
   user  system elapsed 
 20.900   0.600  21.552 

name	user	system	elapsed
birewire.analysis.bipartite	0.052	0.072	0.124
birewire.analysis.dsg	0.028	0.008	0.037
birewire.analysis.undirected	87.912	0.036	88.127
birewire.bipartite.from.incidence	0.000	0.012	0.010
birewire.build.dsg	0.012	0.000	0.013
birewire.induced.bipartite	0.004	0.000	0.003
birewire.rewire.bipartite	0.008	0.004	0.010
birewire.rewire.bipartite.and.projections	0.068	0.008	0.078
birewire.rewire.dsg	0.004	0.000	0.004
birewire.rewire.undirected	0.980	0.020	0.999
birewire.similarity	0.008	0.000	0.008
birewire.similarity.dsg	0.020	0.000	0.018
birewire.visual.monitoring.bipartite	6.800	0.016	6.826
birewire.visual.monitoring.dsg	42.536	0.004	42.633
birewire.visual.monitoring.undirected	14.248	0.056	14.330