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CHECK report for BiRewire on malbec1

This page was generated on 2020-08-11 11:19:32 -0400 (Tue, 11 Aug 2020).

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 181/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.21.0
Andrea Gobbi
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: master
Last Commit: 7ab05ed
Last Changed Date: 2020-04-27 14:36:26 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.21.0
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_3.21.0.tar.gz
StartedAt: 2020-08-11 00:22:19 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 00:25:53 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 213.3 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_3.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiRewire.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘3.21.0’
* 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          77.804  0.028  77.951
birewire.visual.monitoring.dsg        39.876  0.008  39.930
birewire.visual.monitoring.undirected 11.472  0.032  11.512
birewire.visual.monitoring.bipartite   7.988  0.004   8.017
* 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 4.0.2 (2020-06-22) -- "Taking Off Again"
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: 11.7706605455448
Epoch: Iteration #200 error is: 0.539891705506094
Epoch: Iteration #300 error is: 0.281723793275961
Epoch: Iteration #400 error is: 0.272717899494026
Epoch: Iteration #500 error is: 0.253717196755341
Epoch: Iteration #600 error is: 0.251337516009092
Epoch: Iteration #700 error is: 0.250943345729286
Epoch: Iteration #800 error is: 0.250840937810415
Epoch: Iteration #900 error is: 0.250829569509739
Epoch: Iteration #1000 error is: 0.250828951660419
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.63430260123236
Epoch: Iteration #200 error is: 0.523354456552008
Epoch: Iteration #300 error is: 0.276314408772116
Epoch: Iteration #400 error is: 0.257522898504526
Epoch: Iteration #500 error is: 0.252802157245459
Epoch: Iteration #600 error is: 0.252643482172102
Epoch: Iteration #700 error is: 0.252542925365354
Epoch: Iteration #800 error is: 0.25232896584167
Epoch: Iteration #900 error is: 0.251794442125802
Epoch: Iteration #1000 error is: 0.25106170603306
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.3640686106556
Epoch: Iteration #200 error is: 0.506057101469427
Epoch: Iteration #300 error is: 0.281788718174285
Epoch: Iteration #400 error is: 0.271238171775999
Epoch: Iteration #500 error is: 0.263477880174103
Epoch: Iteration #600 error is: 0.25597293862416
Epoch: Iteration #700 error is: 0.253752251694696
Epoch: Iteration #800 error is: 0.252085142557692
Epoch: Iteration #900 error is: 0.251012627481753
Epoch: Iteration #1000 error is: 0.25084483657705
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.7555691001364
Epoch: Iteration #200 error is: 0.255664357888752
Epoch: Iteration #300 error is: 0.250823906386837
Epoch: Iteration #400 error is: 0.250823444118844
Epoch: Iteration #500 error is: 0.25082312549564
Epoch: Iteration #600 error is: 0.250822793125691
Epoch: Iteration #700 error is: 0.250822563324448
Epoch: Iteration #800 error is: 0.250822449909087
Epoch: Iteration #900 error is: 0.25082240518343
Epoch: Iteration #1000 error is: 0.25082238680107
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.9834194648281
Epoch: Iteration #200 error is: 0.523406658364769
Epoch: Iteration #300 error is: 0.31129032073101
Epoch: Iteration #400 error is: 0.272270742516288
Epoch: Iteration #500 error is: 0.257391382228346
Epoch: Iteration #600 error is: 0.254188274614264
Epoch: Iteration #700 error is: 0.253388155504185
Epoch: Iteration #800 error is: 0.252921638000065
Epoch: Iteration #900 error is: 0.252336547855088
Epoch: Iteration #1000 error is: 0.251996162694583
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.8345831325138
Epoch: Iteration #200 error is: 0.480749266211055
Epoch: Iteration #300 error is: 0.29940544393413
Epoch: Iteration #400 error is: 0.26641676355631
Epoch: Iteration #500 error is: 0.257090617996206
Epoch: Iteration #600 error is: 0.253885717077334
Epoch: Iteration #700 error is: 0.252704195357419
Epoch: Iteration #800 error is: 0.252326791946607
Epoch: Iteration #900 error is: 0.252193950498646
Epoch: Iteration #1000 error is: 0.252120501022183
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.8125862588509
Epoch: Iteration #200 error is: 0.281483066019496
Epoch: Iteration #300 error is: 0.252276575484489
Epoch: Iteration #400 error is: 0.251936028633702
Epoch: Iteration #500 error is: 0.251934617306214
Epoch: Iteration #600 error is: 0.251934615803094
Epoch: Iteration #700 error is: 0.251934615232117
Epoch: Iteration #800 error is: 0.251934614373007
Epoch: Iteration #900 error is: 0.251934613235457
Epoch: Iteration #1000 error is: 0.251934611823852
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.80716767895865
Epoch: Iteration #200 error is: 0.606055189016879
Epoch: Iteration #300 error is: 0.38474876899099
Epoch: Iteration #400 error is: 0.297284390870768
Epoch: Iteration #500 error is: 0.278553801921612
Epoch: Iteration #600 error is: 0.269396390942081
Epoch: Iteration #700 error is: 0.261248996846566
Epoch: Iteration #800 error is: 0.25813707374945
Epoch: Iteration #900 error is: 0.257274312086302
Epoch: Iteration #1000 error is: 0.256966228128968


RUNIT TEST PROTOCOL -- Tue Aug 11 00:25:49 2020 
*********************************************** 
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 
 23.672   0.684  24.403 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0520.0680.120
birewire.analysis.dsg0.0320.0040.038
birewire.analysis.undirected77.804 0.02877.951
birewire.bipartite.from.incidence0.0040.0080.011
birewire.build.dsg0.0080.0040.008
birewire.induced.bipartite0.0000.0000.002
birewire.rewire.bipartite0.0080.0040.009
birewire.rewire.bipartite.and.projections0.0760.0000.075
birewire.rewire.dsg0.0040.0000.003
birewire.rewire.undirected0.7720.0240.795
birewire.similarity0.1600.0040.167
birewire.similarity.dsg0.020.000.02
birewire.visual.monitoring.bipartite7.9880.0048.017
birewire.visual.monitoring.dsg39.876 0.00839.930
birewire.visual.monitoring.undirected11.472 0.03211.512