Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-19 12:04:24 -0400 (Tue, 19 Oct 2021).

CHECK results for BiRewire on nebbiolo2

To the developers/maintainers of the BiRewire package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiRewire.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 193/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.25.0  (landing page)
Andrea Gobbi
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: master
git_last_commit: 5f73ade
git_last_commit_date: 2021-05-19 12:00:40 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiRewire
Version: 3.25.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiRewire_3.25.0.tar.gz
StartedAt: 2021-10-18 19:17:24 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 19:20:15 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 171.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiRewire_3.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiRewire.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.25.0’
* 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-3.14-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          66.588  0.356  66.947
birewire.visual.monitoring.dsg        28.180  0.060  28.241
birewire.visual.monitoring.undirected 10.264  0.052  10.317
* 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-3.14-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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]
 1066 |   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]
 1149 |   if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) {
      |               ~^~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: 10.4335375050892
Epoch: Iteration #200 error is: 0.697748526532519
Epoch: Iteration #300 error is: 0.325303486972554
Epoch: Iteration #400 error is: 0.275329248149201
Epoch: Iteration #500 error is: 0.269018701970212
Epoch: Iteration #600 error is: 0.264795201170325
Epoch: Iteration #700 error is: 0.26122366478635
Epoch: Iteration #800 error is: 0.258702114034101
Epoch: Iteration #900 error is: 0.255597500180659
Epoch: Iteration #1000 error is: 0.253209367395741
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.73437502536667
Epoch: Iteration #200 error is: 0.259411155435902
Epoch: Iteration #300 error is: 0.252278153311232
Epoch: Iteration #400 error is: 0.252016761250087
Epoch: Iteration #500 error is: 0.251939054433559
Epoch: Iteration #600 error is: 0.251936432830063
Epoch: Iteration #700 error is: 0.251936419363494
Epoch: Iteration #800 error is: 0.251936419276787
Epoch: Iteration #900 error is: 0.251936419177702
Epoch: Iteration #1000 error is: 0.251936419045518
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.2708110239457
Epoch: Iteration #200 error is: 0.458347574664962
Epoch: Iteration #300 error is: 0.281876587226842
Epoch: Iteration #400 error is: 0.255012584301013
Epoch: Iteration #500 error is: 0.253222179386107
Epoch: Iteration #600 error is: 0.252373344335604
Epoch: Iteration #700 error is: 0.25195760793525
Epoch: Iteration #800 error is: 0.251938030093127
Epoch: Iteration #900 error is: 0.251937682542086
Epoch: Iteration #1000 error is: 0.251937614482072
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.20476454839813
Epoch: Iteration #200 error is: 0.25299979337539
Epoch: Iteration #300 error is: 0.2519300300129
Epoch: Iteration #400 error is: 0.251929796562046
Epoch: Iteration #500 error is: 0.251929792400995
Epoch: Iteration #600 error is: 0.251929785119192
Epoch: Iteration #700 error is: 0.251929774173191
Epoch: Iteration #800 error is: 0.251929759567924
Epoch: Iteration #900 error is: 0.251929741265571
Epoch: Iteration #1000 error is: 0.251929719203786
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.122315375166
Epoch: Iteration #200 error is: 0.417220203451447
Epoch: Iteration #300 error is: 0.276471627691768
Epoch: Iteration #400 error is: 0.253287875962152
Epoch: Iteration #500 error is: 0.252599522777639
Epoch: Iteration #600 error is: 0.252514629814713
Epoch: Iteration #700 error is: 0.252373540415192
Epoch: Iteration #800 error is: 0.252146213350085
Epoch: Iteration #900 error is: 0.251978606021864
Epoch: Iteration #1000 error is: 0.251941148714227
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 17.0453175638249
Epoch: Iteration #200 error is: 0.264063146408784
Epoch: Iteration #300 error is: 0.250824332548471
Epoch: Iteration #400 error is: 0.250823713521127
Epoch: Iteration #500 error is: 0.250823094080554
Epoch: Iteration #600 error is: 0.250822029949939
Epoch: Iteration #700 error is: 0.250820935212382
Epoch: Iteration #800 error is: 0.250820346855654
Epoch: Iteration #900 error is: 0.250820164957206
Epoch: Iteration #1000 error is: 0.250820114322556
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.95718179174246
Epoch: Iteration #200 error is: 0.27774426955424
Epoch: Iteration #300 error is: 0.251090613184875
Epoch: Iteration #400 error is: 0.250830001792955
Epoch: Iteration #500 error is: 0.250829868507285
Epoch: Iteration #600 error is: 0.250829693247025
Epoch: Iteration #700 error is: 0.25082936820015
Epoch: Iteration #800 error is: 0.250828814332798
Epoch: Iteration #900 error is: 0.25082797937293
Epoch: Iteration #1000 error is: 0.250826981690646
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 15.9977630673734
Epoch: Iteration #200 error is: 0.468544155968768
Epoch: Iteration #300 error is: 0.289541581854798
Epoch: Iteration #400 error is: 0.277359770380176
Epoch: Iteration #500 error is: 0.268504238691999
Epoch: Iteration #600 error is: 0.254759916547926
Epoch: Iteration #700 error is: 0.252654863107469
Epoch: Iteration #800 error is: 0.252113270096377
Epoch: Iteration #900 error is: 0.251568722352658
Epoch: Iteration #1000 error is: 0.251110087040483


RUNIT TEST PROTOCOL -- Mon Oct 18 19:20:12 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 
 16.162   0.465  16.611 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0540.0590.115
birewire.analysis.dsg0.0290.0080.036
birewire.analysis.undirected66.588 0.35666.947
birewire.bipartite.from.incidence0.0070.0040.010
birewire.build.dsg0.0090.0000.008
birewire.induced.bipartite0.0030.0000.003
birewire.rewire.bipartite0.0040.0040.009
birewire.rewire.bipartite.and.projections0.0710.0080.080
birewire.rewire.dsg0.0030.0000.003
birewire.rewire.undirected0.5510.0320.583
birewire.similarity0.0040.0040.009
birewire.similarity.dsg0.0110.0080.019
birewire.visual.monitoring.bipartite4.6000.0164.616
birewire.visual.monitoring.dsg28.180 0.06028.241
birewire.visual.monitoring.undirected10.264 0.05210.317