Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).

CHECK results for BiRewire on nebbiolo1

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 194/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.24.0  (landing page)
Andrea Gobbi
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: RELEASE_3_13
git_last_commit: 6a27de6
git_last_commit_date: 2021-05-19 12:00:40 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiRewire
Version: 3.24.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiRewire_3.24.0.tar.gz
StartedAt: 2021-10-14 09:03:54 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:06:46 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 172.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiRewire_3.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘3.24.0’
* 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-3.13-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          64.929  0.167  65.102
birewire.visual.monitoring.dsg        27.683  0.056  27.740
birewire.visual.monitoring.undirected  9.558  0.040   9.611
* 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-3.13-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.c -o interface.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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: 17.8463574158693
Epoch: Iteration #200 error is: 1.00528483904162
Epoch: Iteration #300 error is: 0.403417266061403
Epoch: Iteration #400 error is: 0.292698712910508
Epoch: Iteration #500 error is: 0.271271449864765
Epoch: Iteration #600 error is: 0.263481596137533
Epoch: Iteration #700 error is: 0.26037936251555
Epoch: Iteration #800 error is: 0.258292620710633
Epoch: Iteration #900 error is: 0.256452945366032
Epoch: Iteration #1000 error is: 0.254863949543748
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.3925713447589
Epoch: Iteration #200 error is: 0.923846194908076
Epoch: Iteration #300 error is: 0.444817629264364
Epoch: Iteration #400 error is: 0.287825555917287
Epoch: Iteration #500 error is: 0.273145471751798
Epoch: Iteration #600 error is: 0.267147131297912
Epoch: Iteration #700 error is: 0.262041987413647
Epoch: Iteration #800 error is: 0.256701007204662
Epoch: Iteration #900 error is: 0.254176486547829
Epoch: Iteration #1000 error is: 0.253843424923458
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.2968810111358
Epoch: Iteration #200 error is: 0.921215982534477
Epoch: Iteration #300 error is: 0.561529478734318
Epoch: Iteration #400 error is: 0.36855033147769
Epoch: Iteration #500 error is: 0.279396345537993
Epoch: Iteration #600 error is: 0.264033470929194
Epoch: Iteration #700 error is: 0.258391862825996
Epoch: Iteration #800 error is: 0.255093428422358
Epoch: Iteration #900 error is: 0.253738683129278
Epoch: Iteration #1000 error is: 0.25310880055536
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.044864296125
Epoch: Iteration #200 error is: 0.453968088780104
Epoch: Iteration #300 error is: 0.276146799973358
Epoch: Iteration #400 error is: 0.255485558124513
Epoch: Iteration #500 error is: 0.251685477884547
Epoch: Iteration #600 error is: 0.251092358669204
Epoch: Iteration #700 error is: 0.250866338739603
Epoch: Iteration #800 error is: 0.250834159298613
Epoch: Iteration #900 error is: 0.250831529133131
Epoch: Iteration #1000 error is: 0.25083130752673
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 25.3199820937147
Epoch: Iteration #200 error is: 0.286599312158033
Epoch: Iteration #300 error is: 0.253700494870565
Epoch: Iteration #400 error is: 0.252392033519545
Epoch: Iteration #500 error is: 0.251938276620834
Epoch: Iteration #600 error is: 0.251936938900726
Epoch: Iteration #700 error is: 0.251936693929833
Epoch: Iteration #800 error is: 0.251936684836777
Epoch: Iteration #900 error is: 0.251936684707904
Epoch: Iteration #1000 error is: 0.251936684647443
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.3096202521307
Epoch: Iteration #200 error is: 0.546907657972712
Epoch: Iteration #300 error is: 0.306569917156515
Epoch: Iteration #400 error is: 0.268001381090087
Epoch: Iteration #500 error is: 0.25870341496316
Epoch: Iteration #600 error is: 0.254833555144435
Epoch: Iteration #700 error is: 0.253926549618181
Epoch: Iteration #800 error is: 0.253830310677659
Epoch: Iteration #900 error is: 0.253815462254545
Epoch: Iteration #1000 error is: 0.253808317266062
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 18.9026439379208
Epoch: Iteration #200 error is: 0.26931107780931
Epoch: Iteration #300 error is: 0.252984577484852
Epoch: Iteration #400 error is: 0.251958575217056
Epoch: Iteration #500 error is: 0.251935162699281
Epoch: Iteration #600 error is: 0.251935029648532
Epoch: Iteration #700 error is: 0.251935029304857
Epoch: Iteration #800 error is: 0.251935028805651
Epoch: Iteration #900 error is: 0.25193502811215
Epoch: Iteration #1000 error is: 0.251935027229526
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 24.5715496744224
Epoch: Iteration #200 error is: 0.370946711265956
Epoch: Iteration #300 error is: 0.270977923212868
Epoch: Iteration #400 error is: 0.254349739803354
Epoch: Iteration #500 error is: 0.252753624914369
Epoch: Iteration #600 error is: 0.251382603414836
Epoch: Iteration #700 error is: 0.25089215952148
Epoch: Iteration #800 error is: 0.250834302188001
Epoch: Iteration #900 error is: 0.250830240474623
Epoch: Iteration #1000 error is: 0.250829994849339


RUNIT TEST PROTOCOL -- Thu Oct 14 09:06:43 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 
 16.826   2.144  18.960 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0700.2670.337
birewire.analysis.dsg0.0190.0160.036
birewire.analysis.undirected64.929 0.16765.102
birewire.bipartite.from.incidence0.0040.0280.032
birewire.build.dsg0.0080.0000.008
birewire.induced.bipartite0.0020.0000.002
birewire.rewire.bipartite0.0010.0310.031
birewire.rewire.bipartite.and.projections0.0630.0120.076
birewire.rewire.dsg0.0040.0000.004
birewire.rewire.undirected0.4920.0560.549
birewire.similarity0.0080.0000.008
birewire.similarity.dsg0.0150.0040.018
birewire.visual.monitoring.bipartite4.4730.0244.497
birewire.visual.monitoring.dsg27.683 0.05627.740
birewire.visual.monitoring.undirected9.5580.0409.611