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CHECK report for BiRewire on malbec1

This page was generated on 2021-02-22 12:28:45 -0500 (Mon, 22 Feb 2021).

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 191/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.22.0
Andrea Gobbi
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_12
Last Commit: 161ba9f
Last Changed Date: 2020-10-27 10:52:46 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiRewire_3.22.0.tar.gz
StartedAt: 2021-02-22 00:01:44 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 00:05:38 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 233.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiRewire_3.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-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 ‘3.22.0’
* 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-3.12-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          86.072  0.032  86.211
birewire.visual.monitoring.dsg        46.404  0.016  46.527
birewire.visual.monitoring.undirected 14.208  0.084  14.314
birewire.visual.monitoring.bipartite   7.892  0.012   7.912
* 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-3.12-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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: 8.23165191031115
Epoch: Iteration #200 error is: 0.256494751568297
Epoch: Iteration #300 error is: 0.251933632760202
Epoch: Iteration #400 error is: 0.251929300729976
Epoch: Iteration #500 error is: 0.251929293146145
Epoch: Iteration #600 error is: 0.251929280729277
Epoch: Iteration #700 error is: 0.251929263740275
Epoch: Iteration #800 error is: 0.251929242216655
Epoch: Iteration #900 error is: 0.251929216116527
Epoch: Iteration #1000 error is: 0.251929185352388
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.3260378628701
Epoch: Iteration #200 error is: 0.287252259855531
Epoch: Iteration #300 error is: 0.251014723874511
Epoch: Iteration #400 error is: 0.25083252782009
Epoch: Iteration #500 error is: 0.2508283328596
Epoch: Iteration #600 error is: 0.250828219456021
Epoch: Iteration #700 error is: 0.250828055929041
Epoch: Iteration #800 error is: 0.250827856053527
Epoch: Iteration #900 error is: 0.250827645905013
Epoch: Iteration #1000 error is: 0.25082745120338
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.7111745090929
Epoch: Iteration #200 error is: 0.36427542233881
Epoch: Iteration #300 error is: 0.274775922382084
Epoch: Iteration #400 error is: 0.263826697682289
Epoch: Iteration #500 error is: 0.256957946934951
Epoch: Iteration #600 error is: 0.253202134298162
Epoch: Iteration #700 error is: 0.252317655216944
Epoch: Iteration #800 error is: 0.252171212720283
Epoch: Iteration #900 error is: 0.25210547041957
Epoch: Iteration #1000 error is: 0.252052473497221
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.8495743348114
Epoch: Iteration #200 error is: 0.52957648669611
Epoch: Iteration #300 error is: 0.343082359006803
Epoch: Iteration #400 error is: 0.285674480923366
Epoch: Iteration #500 error is: 0.267996462737662
Epoch: Iteration #600 error is: 0.256998275842914
Epoch: Iteration #700 error is: 0.252975805733554
Epoch: Iteration #800 error is: 0.252260836083216
Epoch: Iteration #900 error is: 0.252085054268259
Epoch: Iteration #1000 error is: 0.252002840752034
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.9416667651936
Epoch: Iteration #200 error is: 0.397297034768261
Epoch: Iteration #300 error is: 0.275038561084835
Epoch: Iteration #400 error is: 0.264955474084164
Epoch: Iteration #500 error is: 0.258722356119155
Epoch: Iteration #600 error is: 0.253209796649282
Epoch: Iteration #700 error is: 0.251984971390462
Epoch: Iteration #800 error is: 0.251943140579456
Epoch: Iteration #900 error is: 0.251939453132914
Epoch: Iteration #1000 error is: 0.251938395069592
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 18.5298114065869
Epoch: Iteration #200 error is: 0.374941929994723
Epoch: Iteration #300 error is: 0.278561469016766
Epoch: Iteration #400 error is: 0.253259226644414
Epoch: Iteration #500 error is: 0.252733365475963
Epoch: Iteration #600 error is: 0.252646329464954
Epoch: Iteration #700 error is: 0.25259110220741
Epoch: Iteration #800 error is: 0.252508064547611
Epoch: Iteration #900 error is: 0.252340852592679
Epoch: Iteration #1000 error is: 0.252095717498559
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.18714836914454
Epoch: Iteration #200 error is: 0.377092711590228
Epoch: Iteration #300 error is: 0.278918085091611
Epoch: Iteration #400 error is: 0.266600068571661
Epoch: Iteration #500 error is: 0.25979559682584
Epoch: Iteration #600 error is: 0.253036388592482
Epoch: Iteration #700 error is: 0.252130451393909
Epoch: Iteration #800 error is: 0.252039642961987
Epoch: Iteration #900 error is: 0.251993780817718
Epoch: Iteration #1000 error is: 0.251963550775401
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.96094090139182
Epoch: Iteration #200 error is: 0.425055524713345
Epoch: Iteration #300 error is: 0.324769015410901
Epoch: Iteration #400 error is: 0.289192149558835
Epoch: Iteration #500 error is: 0.274337599519892
Epoch: Iteration #600 error is: 0.260303935592624
Epoch: Iteration #700 error is: 0.256780480742655
Epoch: Iteration #800 error is: 0.255894518391825
Epoch: Iteration #900 error is: 0.255083551377866
Epoch: Iteration #1000 error is: 0.254217993232032


RUNIT TEST PROTOCOL -- Mon Feb 22 00:05:34 2021 
*********************************************** 
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 
 26.232   0.612  26.933 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0600.0880.149
birewire.analysis.dsg0.0280.0080.036
birewire.analysis.undirected86.072 0.03286.211
birewire.bipartite.from.incidence0.0040.0080.011
birewire.build.dsg0.0080.0000.008
birewire.induced.bipartite0.0000.0000.003
birewire.rewire.bipartite0.0000.0080.010
birewire.rewire.bipartite.and.projections0.0800.0000.081
birewire.rewire.dsg0.0040.0000.003
birewire.rewire.undirected0.7040.0160.721
birewire.similarity0.1520.0000.152
birewire.similarity.dsg0.0320.0000.034
birewire.visual.monitoring.bipartite7.8920.0127.912
birewire.visual.monitoring.dsg46.404 0.01646.527
birewire.visual.monitoring.undirected14.208 0.08414.314