Package: BiRewire

Version: 3.14.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiRewire_3.14.0.tar.gz

StartedAt: 2019-04-15 22:32:52 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:36:04 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 192.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiRewire.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiRewire_3.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BiRewire.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘3.14.0’
* 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-3.8-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          71.480  0.020  71.598
birewire.visual.monitoring.dsg        38.824  0.008  38.906
birewire.visual.monitoring.undirected 11.284  0.036  11.334
birewire.visual.monitoring.bipartite   6.152  0.004   6.172
* 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-3.8-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BiRewire
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (BiRewire)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: 12.2338246289166
Epoch: Iteration #200 error is: 0.621053176184411
Epoch: Iteration #300 error is: 0.349252221322112
Epoch: Iteration #400 error is: 0.259473270773171
Epoch: Iteration #500 error is: 0.25474077816735
Epoch: Iteration #600 error is: 0.25312454346954
Epoch: Iteration #700 error is: 0.252572355904492
Epoch: Iteration #800 error is: 0.252409929082585
Epoch: Iteration #900 error is: 0.252315227551624
Epoch: Iteration #1000 error is: 0.252223637370485
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.9684784826767
Epoch: Iteration #200 error is: 0.291803380425309
Epoch: Iteration #300 error is: 0.253911335109187
Epoch: Iteration #400 error is: 0.252072452883859
Epoch: Iteration #500 error is: 0.251936536337479
Epoch: Iteration #600 error is: 0.251936443015709
Epoch: Iteration #700 error is: 0.251936427328574
Epoch: Iteration #800 error is: 0.251936426728322
Epoch: Iteration #900 error is: 0.251936426649127
Epoch: Iteration #1000 error is: 0.251936426546149
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.50295551442765
Epoch: Iteration #200 error is: 0.280505845516845
Epoch: Iteration #300 error is: 0.25085568876103
Epoch: Iteration #400 error is: 0.250829733233056
Epoch: Iteration #500 error is: 0.250829701040956
Epoch: Iteration #600 error is: 0.250829700202906
Epoch: Iteration #700 error is: 0.250829698734981
Epoch: Iteration #800 error is: 0.250829696598408
Epoch: Iteration #900 error is: 0.250829693621196
Epoch: Iteration #1000 error is: 0.25082968927676
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.8182300954891
Epoch: Iteration #200 error is: 0.389237199603079
Epoch: Iteration #300 error is: 0.269075465149707
Epoch: Iteration #400 error is: 0.252841791390153
Epoch: Iteration #500 error is: 0.252535459216295
Epoch: Iteration #600 error is: 0.252336138406464
Epoch: Iteration #700 error is: 0.251558192112622
Epoch: Iteration #800 error is: 0.250859705387079
Epoch: Iteration #900 error is: 0.250828316151404
Epoch: Iteration #1000 error is: 0.250828193206697
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.0674757238298
Epoch: Iteration #200 error is: 0.279924160556207
Epoch: Iteration #300 error is: 0.250897663577404
Epoch: Iteration #400 error is: 0.250829840851156
Epoch: Iteration #500 error is: 0.250829377236706
Epoch: Iteration #600 error is: 0.250829078542829
Epoch: Iteration #700 error is: 0.250828636442982
Epoch: Iteration #800 error is: 0.250828076616929
Epoch: Iteration #900 error is: 0.25082747655249
Epoch: Iteration #1000 error is: 0.250826948704014
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.5476789651005
Epoch: Iteration #200 error is: 0.726741538036746
Epoch: Iteration #300 error is: 0.366754797605178
Epoch: Iteration #400 error is: 0.262167883038099
Epoch: Iteration #500 error is: 0.253206841685048
Epoch: Iteration #600 error is: 0.251824024988932
Epoch: Iteration #700 error is: 0.251508251519867
Epoch: Iteration #800 error is: 0.251198269838208
Epoch: Iteration #900 error is: 0.250970540405855
Epoch: Iteration #1000 error is: 0.250869323861132
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.0696335508513
Epoch: Iteration #200 error is: 0.379222387110479
Epoch: Iteration #300 error is: 0.278682989502179
Epoch: Iteration #400 error is: 0.264068903216398
Epoch: Iteration #500 error is: 0.252395505738041
Epoch: Iteration #600 error is: 0.251948971811004
Epoch: Iteration #700 error is: 0.251937654516179
Epoch: Iteration #800 error is: 0.251937485704718
Epoch: Iteration #900 error is: 0.251937432468231
Epoch: Iteration #1000 error is: 0.251937421362036
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.6593252991989
Epoch: Iteration #200 error is: 0.357171670119633
Epoch: Iteration #300 error is: 0.277567202848731
Epoch: Iteration #400 error is: 0.263563704879019
Epoch: Iteration #500 error is: 0.261420093722841
Epoch: Iteration #600 error is: 0.258710476974349
Epoch: Iteration #700 error is: 0.254278892407051
Epoch: Iteration #800 error is: 0.251683237599455
Epoch: Iteration #900 error is: 0.250875453118571
Epoch: Iteration #1000 error is: 0.250834437246762


RUNIT TEST PROTOCOL -- Mon Apr 15 22:36:01 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 
 20.772   0.584  21.398 

name	user	system	elapsed
birewire.analysis.bipartite	0.060	0.080	0.137
birewire.analysis.dsg	0.06	0.00	0.06
birewire.analysis.undirected	71.480	0.020	71.598
birewire.bipartite.from.incidence	0.004	0.012	0.016
birewire.build.dsg	0.012	0.000	0.013
birewire.induced.bipartite	0.004	0.000	0.004
birewire.rewire.bipartite	0.012	0.004	0.015
birewire.rewire.bipartite.and.projections	0.156	0.004	0.162
birewire.rewire.dsg	0.008	0.000	0.005
birewire.rewire.undirected	0.924	0.020	0.948
birewire.similarity	0.012	0.000	0.011
birewire.similarity.dsg	0.032	0.000	0.035
birewire.visual.monitoring.bipartite	6.152	0.004	6.172
birewire.visual.monitoring.dsg	38.824	0.008	38.906
birewire.visual.monitoring.undirected	11.284	0.036	11.334