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CHECK report for BiRewire on malbec2

This page was generated on 2019-10-16 12:03:19 -0400 (Wed, 16 Oct 2019).

Package 173/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.16.0
Andrea Gobbi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_9
Last Commit: 70f40cb
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.16.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiRewire_3.16.0.tar.gz
StartedAt: 2019-10-16 00:09:03 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:12:39 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 216.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiRewire_3.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiRewire.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.16.0’
* 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-3.9-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          82.244  0.059  82.385
birewire.visual.monitoring.dsg        40.922  0.000  40.929
birewire.visual.monitoring.undirected 14.549  0.084  14.635
birewire.visual.monitoring.bipartite   6.183  0.012   6.195
* 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-3.9-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

Tests output

BiRewire.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 10.3908252335878
Epoch: Iteration #200 error is: 0.603933137373837
Epoch: Iteration #300 error is: 0.368989697785443
Epoch: Iteration #400 error is: 0.283376708232868
Epoch: Iteration #500 error is: 0.269929367954523
Epoch: Iteration #600 error is: 0.260194649194974
Epoch: Iteration #700 error is: 0.254468979214778
Epoch: Iteration #800 error is: 0.252840293376382
Epoch: Iteration #900 error is: 0.252665217555947
Epoch: Iteration #1000 error is: 0.252650814631265
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.4789025013002
Epoch: Iteration #200 error is: 0.292906370460677
Epoch: Iteration #300 error is: 0.256495780276076
Epoch: Iteration #400 error is: 0.252685821433654
Epoch: Iteration #500 error is: 0.252495537339849
Epoch: Iteration #600 error is: 0.252226596283303
Epoch: Iteration #700 error is: 0.251962766847063
Epoch: Iteration #800 error is: 0.251937335481808
Epoch: Iteration #900 error is: 0.251937010594812
Epoch: Iteration #1000 error is: 0.251937009453676
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.0808141723035
Epoch: Iteration #200 error is: 0.526830891276013
Epoch: Iteration #300 error is: 0.269350923794966
Epoch: Iteration #400 error is: 0.253717890709085
Epoch: Iteration #500 error is: 0.252258628023475
Epoch: Iteration #600 error is: 0.252041074043444
Epoch: Iteration #700 error is: 0.251971602738202
Epoch: Iteration #800 error is: 0.251945248042803
Epoch: Iteration #900 error is: 0.251938753189644
Epoch: Iteration #1000 error is: 0.251937781377317
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.0517749771783
Epoch: Iteration #200 error is: 0.341995482699499
Epoch: Iteration #300 error is: 0.25408055465722
Epoch: Iteration #400 error is: 0.25230553817085
Epoch: Iteration #500 error is: 0.251169770794536
Epoch: Iteration #600 error is: 0.250837820898738
Epoch: Iteration #700 error is: 0.250828157122976
Epoch: Iteration #800 error is: 0.250828096986315
Epoch: Iteration #900 error is: 0.250828095481658
Epoch: Iteration #1000 error is: 0.250828093830634
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.1040854575306
Epoch: Iteration #200 error is: 0.323652499340613
Epoch: Iteration #300 error is: 0.265427748177227
Epoch: Iteration #400 error is: 0.256461360783814
Epoch: Iteration #500 error is: 0.253807506012801
Epoch: Iteration #600 error is: 0.251230543615146
Epoch: Iteration #700 error is: 0.250835664764788
Epoch: Iteration #800 error is: 0.250830882053901
Epoch: Iteration #900 error is: 0.250830749152743
Epoch: Iteration #1000 error is: 0.250830594282612
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 17.1415726946528
Epoch: Iteration #200 error is: 0.643344576904952
Epoch: Iteration #300 error is: 0.288879307922153
Epoch: Iteration #400 error is: 0.268731906323279
Epoch: Iteration #500 error is: 0.259227582575993
Epoch: Iteration #600 error is: 0.254405040323863
Epoch: Iteration #700 error is: 0.25393021021689
Epoch: Iteration #800 error is: 0.253756625245469
Epoch: Iteration #900 error is: 0.253531570022557
Epoch: Iteration #1000 error is: 0.252923257445271
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.4683419908195
Epoch: Iteration #200 error is: 0.421995559255397
Epoch: Iteration #300 error is: 0.28121328358525
Epoch: Iteration #400 error is: 0.258785249051593
Epoch: Iteration #500 error is: 0.255190827598937
Epoch: Iteration #600 error is: 0.253635807697737
Epoch: Iteration #700 error is: 0.252123638196182
Epoch: Iteration #800 error is: 0.25105192519111
Epoch: Iteration #900 error is: 0.250846529627481
Epoch: Iteration #1000 error is: 0.25083370715152
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.37762158611728
Epoch: Iteration #200 error is: 0.265249949544936
Epoch: Iteration #300 error is: 0.251999535908093
Epoch: Iteration #400 error is: 0.251940269843858
Epoch: Iteration #500 error is: 0.251935161898225
Epoch: Iteration #600 error is: 0.251935145923635
Epoch: Iteration #700 error is: 0.251935145536479
Epoch: Iteration #800 error is: 0.251935144969761
Epoch: Iteration #900 error is: 0.25193514422308
Epoch: Iteration #1000 error is: 0.251935143302584


RUNIT TEST PROTOCOL -- Wed Oct 16 00:12:36 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 
 21.432   0.551  21.983 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0960.1000.198
birewire.analysis.dsg0.0500.0040.055
birewire.analysis.undirected82.244 0.05982.385
birewire.bipartite.from.incidence0.0030.0080.011
birewire.build.dsg0.0080.0000.007
birewire.induced.bipartite0.0030.0000.002
birewire.rewire.bipartite0.0060.0040.010
birewire.rewire.bipartite.and.projections0.0800.0040.084
birewire.rewire.dsg0.0040.0000.004
birewire.rewire.undirected0.5250.0160.541
birewire.similarity0.0070.0000.007
birewire.similarity.dsg0.0190.0000.019
birewire.visual.monitoring.bipartite6.1830.0126.195
birewire.visual.monitoring.dsg40.922 0.00040.929
birewire.visual.monitoring.undirected14.549 0.08414.635