Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).

CHECK results for BiRewire on machv2

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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.24.0.tar.gz
StartedAt: 2021-10-14 16:51:44 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 16:55:55 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 251.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiRewire’ can be installed ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          71.328  0.197  71.613
birewire.visual.monitoring.dsg        57.689  0.368  58.093
birewire.visual.monitoring.undirected 16.446  0.345  16.802
birewire.visual.monitoring.bipartite   8.981  0.095   9.088
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interface.c -o interface.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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: 19.612639371649
Epoch: Iteration #200 error is: 0.857030717052881
Epoch: Iteration #300 error is: 0.522687185144837
Epoch: Iteration #400 error is: 0.33011123047053
Epoch: Iteration #500 error is: 0.282823579409205
Epoch: Iteration #600 error is: 0.26540228793868
Epoch: Iteration #700 error is: 0.258853848473128
Epoch: Iteration #800 error is: 0.255134423941981
Epoch: Iteration #900 error is: 0.253302996667505
Epoch: Iteration #1000 error is: 0.252610790853235
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.99086239878309
Epoch: Iteration #200 error is: 0.339845691325571
Epoch: Iteration #300 error is: 0.257378700006327
Epoch: Iteration #400 error is: 0.254405738240569
Epoch: Iteration #500 error is: 0.253581229023367
Epoch: Iteration #600 error is: 0.252531486757702
Epoch: Iteration #700 error is: 0.251342977983352
Epoch: Iteration #800 error is: 0.250862029779055
Epoch: Iteration #900 error is: 0.250833565802055
Epoch: Iteration #1000 error is: 0.250832895307298
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.23767000150073
Epoch: Iteration #200 error is: 0.312219039805867
Epoch: Iteration #300 error is: 0.254314437000334
Epoch: Iteration #400 error is: 0.252212707385588
Epoch: Iteration #500 error is: 0.251019291751366
Epoch: Iteration #600 error is: 0.250834672214303
Epoch: Iteration #700 error is: 0.250830610316087
Epoch: Iteration #800 error is: 0.25083045755699
Epoch: Iteration #900 error is: 0.250830316658847
Epoch: Iteration #1000 error is: 0.250830136312183
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.0078414989719
Epoch: Iteration #200 error is: 0.280964587060796
Epoch: Iteration #300 error is: 0.252887095546938
Epoch: Iteration #400 error is: 0.251836270101522
Epoch: Iteration #500 error is: 0.250832859128257
Epoch: Iteration #600 error is: 0.250828123995319
Epoch: Iteration #700 error is: 0.250827881275946
Epoch: Iteration #800 error is: 0.25082754019314
Epoch: Iteration #900 error is: 0.250827156575003
Epoch: Iteration #1000 error is: 0.250826799176581
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.91196347240898
Epoch: Iteration #200 error is: 0.257079442295357
Epoch: Iteration #300 error is: 0.253458868601962
Epoch: Iteration #400 error is: 0.250819359522329
Epoch: Iteration #500 error is: 0.250818978952155
Epoch: Iteration #600 error is: 0.250818504465716
Epoch: Iteration #700 error is: 0.250818194372099
Epoch: Iteration #800 error is: 0.250818069137601
Epoch: Iteration #900 error is: 0.250818018988622
Epoch: Iteration #1000 error is: 0.250817983327716
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 16.9181840525269
Epoch: Iteration #200 error is: 0.60626389315974
Epoch: Iteration #300 error is: 0.349173041021035
Epoch: Iteration #400 error is: 0.299026178924191
Epoch: Iteration #500 error is: 0.278791419318705
Epoch: Iteration #600 error is: 0.270584608783478
Epoch: Iteration #700 error is: 0.26515039861481
Epoch: Iteration #800 error is: 0.255650807002343
Epoch: Iteration #900 error is: 0.252404532836066
Epoch: Iteration #1000 error is: 0.251860673726831
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 8.55801959703656
Epoch: Iteration #200 error is: 0.263889378798895
Epoch: Iteration #300 error is: 0.252463666364801
Epoch: Iteration #400 error is: 0.250914682756689
Epoch: Iteration #500 error is: 0.250827244925779
Epoch: Iteration #600 error is: 0.250827085083931
Epoch: Iteration #700 error is: 0.250826873074398
Epoch: Iteration #800 error is: 0.250826638656496
Epoch: Iteration #900 error is: 0.250826428547183
Epoch: Iteration #1000 error is: 0.250826270783998
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.71823613049876
Epoch: Iteration #200 error is: 0.507525668853669
Epoch: Iteration #300 error is: 0.281271530017402
Epoch: Iteration #400 error is: 0.270168944176129
Epoch: Iteration #500 error is: 0.265339441191442
Epoch: Iteration #600 error is: 0.25438917410257
Epoch: Iteration #700 error is: 0.252368939463213
Epoch: Iteration #800 error is: 0.252234294741005
Epoch: Iteration #900 error is: 0.252104030206734
Epoch: Iteration #1000 error is: 0.252000150503251


RUNIT TEST PROTOCOL -- Thu Oct 14 16:55:46 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 
 26.656   2.476  29.292 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1300.3460.477
birewire.analysis.dsg0.0460.0110.059
birewire.analysis.undirected71.328 0.19771.613
birewire.bipartite.from.incidence0.0110.0380.049
birewire.build.dsg0.0100.0020.011
birewire.induced.bipartite0.0050.0020.006
birewire.rewire.bipartite0.0090.0340.043
birewire.rewire.bipartite.and.projections0.0950.0100.106
birewire.rewire.dsg0.0060.0020.008
birewire.rewire.undirected0.9100.0630.975
birewire.similarity0.0080.0000.009
birewire.similarity.dsg0.0330.0020.035
birewire.visual.monitoring.bipartite8.9810.0959.088
birewire.visual.monitoring.dsg57.689 0.36858.093
birewire.visual.monitoring.undirected16.446 0.34516.802