Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:04:51 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 197/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.26.0  (landing page)
Andrea Gobbi
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: RELEASE_3_14
git_last_commit: 0c583a5
git_last_commit_date: 2021-10-26 12:09:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 3.26.0
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_3.26.0.tar.gz
StartedAt: 2022-01-23 06:43:27 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 06:46:15 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 168.0 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_3.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiRewire.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘3.26.0’
* 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          65.844  0.119  65.966
birewire.visual.monitoring.dsg        26.390  0.021  26.411
birewire.visual.monitoring.undirected  9.531  0.043   9.575
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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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DONE in 0 seconds 
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.0174075612311
Epoch: Iteration #200 error is: 0.735948204562797
Epoch: Iteration #300 error is: 0.4075609644907
Epoch: Iteration #400 error is: 0.282034946961788
Epoch: Iteration #500 error is: 0.265153465368051
Epoch: Iteration #600 error is: 0.260153778949864
Epoch: Iteration #700 error is: 0.255235772917781
Epoch: Iteration #800 error is: 0.252756113461459
Epoch: Iteration #900 error is: 0.252212390375293
Epoch: Iteration #1000 error is: 0.252032199685071
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.70436485455657
Epoch: Iteration #200 error is: 0.272287023377307
Epoch: Iteration #300 error is: 0.252569328334451
Epoch: Iteration #400 error is: 0.250932640327739
Epoch: Iteration #500 error is: 0.250827138164727
Epoch: Iteration #600 error is: 0.250826858279965
Epoch: Iteration #700 error is: 0.250826841763828
Epoch: Iteration #800 error is: 0.250826821525947
Epoch: Iteration #900 error is: 0.250826799514084
Epoch: Iteration #1000 error is: 0.250826779325647
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.48463205520666
Epoch: Iteration #200 error is: 0.282561611259771
Epoch: Iteration #300 error is: 0.254864305622687
Epoch: Iteration #400 error is: 0.253788094619143
Epoch: Iteration #500 error is: 0.253083924762134
Epoch: Iteration #600 error is: 0.251937901447672
Epoch: Iteration #700 error is: 0.251936776380721
Epoch: Iteration #800 error is: 0.251936699859547
Epoch: Iteration #900 error is: 0.251936695089518
Epoch: Iteration #1000 error is: 0.251936694980888
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.8071779394315
Epoch: Iteration #200 error is: 0.489553295512128
Epoch: Iteration #300 error is: 0.271336922126074
Epoch: Iteration #400 error is: 0.261354964224478
Epoch: Iteration #500 error is: 0.254211466500869
Epoch: Iteration #600 error is: 0.252226369378609
Epoch: Iteration #700 error is: 0.25096834018814
Epoch: Iteration #800 error is: 0.250834814996322
Epoch: Iteration #900 error is: 0.250832164115278
Epoch: Iteration #1000 error is: 0.250832056551449
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 24.1351424810365
Epoch: Iteration #200 error is: 0.863900362154973
Epoch: Iteration #300 error is: 0.496674200583234
Epoch: Iteration #400 error is: 0.306161032647045
Epoch: Iteration #500 error is: 0.27601424700699
Epoch: Iteration #600 error is: 0.26343562221419
Epoch: Iteration #700 error is: 0.257627500958921
Epoch: Iteration #800 error is: 0.254680920237966
Epoch: Iteration #900 error is: 0.253002864284409
Epoch: Iteration #1000 error is: 0.252273068442789
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 20.544884292188
Epoch: Iteration #200 error is: 0.747170781596112
Epoch: Iteration #300 error is: 0.330216312991657
Epoch: Iteration #400 error is: 0.273159064626414
Epoch: Iteration #500 error is: 0.264165390019224
Epoch: Iteration #600 error is: 0.254307537540113
Epoch: Iteration #700 error is: 0.252431127375007
Epoch: Iteration #800 error is: 0.252102709451584
Epoch: Iteration #900 error is: 0.2517541327342
Epoch: Iteration #1000 error is: 0.251332552881548
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 14.5558212642947
Epoch: Iteration #200 error is: 0.967072187703565
Epoch: Iteration #300 error is: 0.484277540759314
Epoch: Iteration #400 error is: 0.313333369071185
Epoch: Iteration #500 error is: 0.273185141200307
Epoch: Iteration #600 error is: 0.266798350745381
Epoch: Iteration #700 error is: 0.261108164868655
Epoch: Iteration #800 error is: 0.255207957063641
Epoch: Iteration #900 error is: 0.252659766279159
Epoch: Iteration #1000 error is: 0.252102956520041
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.9487339659734
Epoch: Iteration #200 error is: 0.372031164300346
Epoch: Iteration #300 error is: 0.302712033251827
Epoch: Iteration #400 error is: 0.265915751001612
Epoch: Iteration #500 error is: 0.256170952127215
Epoch: Iteration #600 error is: 0.254790866635828
Epoch: Iteration #700 error is: 0.25343094335305
Epoch: Iteration #800 error is: 0.252056584506856
Epoch: Iteration #900 error is: 0.251162617223575
Epoch: Iteration #1000 error is: 0.250881628863631


RUNIT TEST PROTOCOL -- Sun Jan 23 06:46:11 2022 
*********************************************** 
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 
 15.877   0.427  16.288 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0410.0730.112
birewire.analysis.dsg0.0250.0110.036
birewire.analysis.undirected65.844 0.11965.966
birewire.bipartite.from.incidence0.0010.0080.010
birewire.build.dsg0.0070.0000.007
birewire.induced.bipartite0.0030.0000.002
birewire.rewire.bipartite0.0010.0070.008
birewire.rewire.bipartite.and.projections0.0750.0000.075
birewire.rewire.dsg0.0030.0010.003
birewire.rewire.undirected0.5060.0240.531
birewire.similarity0.0070.0000.008
birewire.similarity.dsg0.0180.0000.018
birewire.visual.monitoring.bipartite4.3900.0074.399
birewire.visual.monitoring.dsg26.390 0.02126.411
birewire.visual.monitoring.undirected9.5310.0439.575