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CHECK report for BiRewire on malbec2

This page was generated on 2020-10-17 11:54:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiRewire PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 187/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.20.0
Andrea Gobbi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_11
Last Commit: 6b3b1f2
Last Changed Date: 2020-04-27 14:36:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.20.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiRewire_3.20.0.tar.gz
StartedAt: 2020-10-16 23:21:10 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:25:04 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 234.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiRewire_3.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BiRewire.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘3.20.0’
* 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-3.11-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
  ‘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
  ‘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
  ‘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 ‘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 ‘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 ‘colorRampPalette’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘text’
Undefined global functions or variables:
  abline colorRampPalette dev.off legend lines par polygon qt
  read.table sd text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "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 (user + system) or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          80.376  0.028  80.406
birewire.visual.monitoring.dsg        43.824  0.004  43.827
birewire.visual.monitoring.undirected 15.034  0.039  15.076
birewire.visual.monitoring.bipartite   6.632  0.016   6.648
* 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-3.11-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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: 10.297257298482
Epoch: Iteration #200 error is: 0.374450350210195
Epoch: Iteration #300 error is: 0.278468482966166
Epoch: Iteration #400 error is: 0.266420399430777
Epoch: Iteration #500 error is: 0.252643447403927
Epoch: Iteration #600 error is: 0.251566612575161
Epoch: Iteration #700 error is: 0.250963677054184
Epoch: Iteration #800 error is: 0.250842391777024
Epoch: Iteration #900 error is: 0.250831768991318
Epoch: Iteration #1000 error is: 0.250831046392554
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.89543776128833
Epoch: Iteration #200 error is: 0.273292242381988
Epoch: Iteration #300 error is: 0.251391195822766
Epoch: Iteration #400 error is: 0.250827549314677
Epoch: Iteration #500 error is: 0.250827480355224
Epoch: Iteration #600 error is: 0.25082729830997
Epoch: Iteration #700 error is: 0.250826872980356
Epoch: Iteration #800 error is: 0.250825958533727
Epoch: Iteration #900 error is: 0.250824505406633
Epoch: Iteration #1000 error is: 0.250823283621274
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.3722100832017
Epoch: Iteration #200 error is: 0.450211217447663
Epoch: Iteration #300 error is: 0.264672252295313
Epoch: Iteration #400 error is: 0.255030996712804
Epoch: Iteration #500 error is: 0.252634087390626
Epoch: Iteration #600 error is: 0.252308729400936
Epoch: Iteration #700 error is: 0.251963846940812
Epoch: Iteration #800 error is: 0.251442019292435
Epoch: Iteration #900 error is: 0.250993032451922
Epoch: Iteration #1000 error is: 0.25085359825547
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.1229131937439
Epoch: Iteration #200 error is: 0.251236921064527
Epoch: Iteration #300 error is: 0.250818683302575
Epoch: Iteration #400 error is: 0.250818409297528
Epoch: Iteration #500 error is: 0.250818122809486
Epoch: Iteration #600 error is: 0.25081795674974
Epoch: Iteration #700 error is: 0.250817882235004
Epoch: Iteration #800 error is: 0.250817839641132
Epoch: Iteration #900 error is: 0.250817798780495
Epoch: Iteration #1000 error is: 0.250817750220799
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.4287793108568
Epoch: Iteration #200 error is: 0.531194988449514
Epoch: Iteration #300 error is: 0.272927249709536
Epoch: Iteration #400 error is: 0.255274080207419
Epoch: Iteration #500 error is: 0.252952892689482
Epoch: Iteration #600 error is: 0.252646517889564
Epoch: Iteration #700 error is: 0.252559837016582
Epoch: Iteration #800 error is: 0.252430858840979
Epoch: Iteration #900 error is: 0.252113604269028
Epoch: Iteration #1000 error is: 0.251437416900669
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.21158572407318
Epoch: Iteration #200 error is: 0.255425995524771
Epoch: Iteration #300 error is: 0.251244200963563
Epoch: Iteration #400 error is: 0.250829195707363
Epoch: Iteration #500 error is: 0.250829035911936
Epoch: Iteration #600 error is: 0.250828709203023
Epoch: Iteration #700 error is: 0.250828131586157
Epoch: Iteration #800 error is: 0.250827257153669
Epoch: Iteration #900 error is: 0.250826241844081
Epoch: Iteration #1000 error is: 0.250825438543912
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.2234505814837
Epoch: Iteration #200 error is: 0.340916351791435
Epoch: Iteration #300 error is: 0.265111312576241
Epoch: Iteration #400 error is: 0.253602284751736
Epoch: Iteration #500 error is: 0.252585302225842
Epoch: Iteration #600 error is: 0.252313084639458
Epoch: Iteration #700 error is: 0.251776266120371
Epoch: Iteration #800 error is: 0.251080390337909
Epoch: Iteration #900 error is: 0.250850269580762
Epoch: Iteration #1000 error is: 0.25083419433195
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.7217952393004
Epoch: Iteration #200 error is: 0.520530690896532
Epoch: Iteration #300 error is: 0.31373052442552
Epoch: Iteration #400 error is: 0.266254717394669
Epoch: Iteration #500 error is: 0.254412604672389
Epoch: Iteration #600 error is: 0.25276483529858
Epoch: Iteration #700 error is: 0.252237679689605
Epoch: Iteration #800 error is: 0.251975964139674
Epoch: Iteration #900 error is: 0.251940089712316
Epoch: Iteration #1000 error is: 0.251938134505641


RUNIT TEST PROTOCOL -- Fri Oct 16 23:25:00 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 
Warning messages:
1: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
2: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
3: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
4: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
5: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
6: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
7: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
8: In if (class(X) == "dist") { :
  the condition has length > 1 and only the first element will be used
> 
> proc.time()
   user  system elapsed 
 24.142   0.632  24.767 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1230.0830.207
birewire.analysis.dsg0.0530.0070.061
birewire.analysis.undirected80.376 0.02880.406
birewire.bipartite.from.incidence0.0100.0080.018
birewire.build.dsg0.0110.0000.012
birewire.induced.bipartite0.0050.0000.005
birewire.rewire.bipartite0.0070.0070.015
birewire.rewire.bipartite.and.projections0.1290.0040.133
birewire.rewire.dsg0.0060.0010.006
birewire.rewire.undirected0.7850.0160.801
birewire.similarity0.1510.0030.155
birewire.similarity.dsg0.0270.0000.027
birewire.visual.monitoring.bipartite6.6320.0166.648
birewire.visual.monitoring.dsg43.824 0.00443.827
birewire.visual.monitoring.undirected15.034 0.03915.076