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CHECK report for BiRewire on nebbiolo1

This page was generated on 2021-03-03 12:11:38 -0500 (Wed, 03 Mar 2021).

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 191/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.22.0
Andrea Gobbi
Snapshot Date: 2021-03-02 14:50:31 -0500 (Tue, 02 Mar 2021)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_12
Last Commit: 161ba9f
Last Changed Date: 2020-10-27 10:52:46 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.22.0
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_3.22.0.tar.gz
StartedAt: 2021-03-02 20:26:07 -0500 (Tue, 02 Mar 2021)
EndedAt: 2021-03-02 20:29:56 -0500 (Tue, 02 Mar 2021)
EllapsedTime: 228.1 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_3.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiRewire.Rcheck’
* using R version 4.0.4 (2021-02-15)
* 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 ‘3.22.0’
* 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          59.822  0.141  59.967
birewire.visual.monitoring.dsg        23.854  0.013  23.878
birewire.visual.monitoring.undirected  8.612  0.059   8.672
* 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

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###
### 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]
 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-3.12-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 4.0.4 (2021-02-15) -- "Lost Library Book"
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: 8.69071579249329
Epoch: Iteration #200 error is: 0.338424867983228
Epoch: Iteration #300 error is: 0.277169943405763
Epoch: Iteration #400 error is: 0.265604534781322
Epoch: Iteration #500 error is: 0.260231289196968
Epoch: Iteration #600 error is: 0.255596743487318
Epoch: Iteration #700 error is: 0.253117494794074
Epoch: Iteration #800 error is: 0.251913016033649
Epoch: Iteration #900 error is: 0.251021821538132
Epoch: Iteration #1000 error is: 0.250843106570186
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.43982988297272
Epoch: Iteration #200 error is: 0.265750806398255
Epoch: Iteration #300 error is: 0.252183604567297
Epoch: Iteration #400 error is: 0.251954578948304
Epoch: Iteration #500 error is: 0.251935231594145
Epoch: Iteration #600 error is: 0.251935185236227
Epoch: Iteration #700 error is: 0.251935184940409
Epoch: Iteration #800 error is: 0.251935184491551
Epoch: Iteration #900 error is: 0.251935183876954
Epoch: Iteration #1000 error is: 0.251935183100709
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.62990873422236
Epoch: Iteration #200 error is: 0.275534924671576
Epoch: Iteration #300 error is: 0.253638943290367
Epoch: Iteration #400 error is: 0.251944745608558
Epoch: Iteration #500 error is: 0.251935249149578
Epoch: Iteration #600 error is: 0.251934873231479
Epoch: Iteration #700 error is: 0.251934872355711
Epoch: Iteration #800 error is: 0.251934871792677
Epoch: Iteration #900 error is: 0.251934870993176
Epoch: Iteration #1000 error is: 0.25193486996992
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.9355538743525
Epoch: Iteration #200 error is: 0.772743640209736
Epoch: Iteration #300 error is: 0.379655088149231
Epoch: Iteration #400 error is: 0.277482612739672
Epoch: Iteration #500 error is: 0.270634840802109
Epoch: Iteration #600 error is: 0.265868640672184
Epoch: Iteration #700 error is: 0.261252811574527
Epoch: Iteration #800 error is: 0.25625640212229
Epoch: Iteration #900 error is: 0.253456121425934
Epoch: Iteration #1000 error is: 0.25251362385141
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.5579705559748
Epoch: Iteration #200 error is: 0.481482243064086
Epoch: Iteration #300 error is: 0.345974976908648
Epoch: Iteration #400 error is: 0.288660595217638
Epoch: Iteration #500 error is: 0.2749408541693
Epoch: Iteration #600 error is: 0.264442839184618
Epoch: Iteration #700 error is: 0.257669735435881
Epoch: Iteration #800 error is: 0.253530472561425
Epoch: Iteration #900 error is: 0.252252486285738
Epoch: Iteration #1000 error is: 0.251991166109287
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.1551342372932
Epoch: Iteration #200 error is: 0.34208857193659
Epoch: Iteration #300 error is: 0.265774409923103
Epoch: Iteration #400 error is: 0.255297394500915
Epoch: Iteration #500 error is: 0.252673066893818
Epoch: Iteration #600 error is: 0.252606358866775
Epoch: Iteration #700 error is: 0.252535161147769
Epoch: Iteration #800 error is: 0.25229311812243
Epoch: Iteration #900 error is: 0.251527473324106
Epoch: Iteration #1000 error is: 0.250879005041924
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.3795844057805
Epoch: Iteration #200 error is: 0.263270674256699
Epoch: Iteration #300 error is: 0.253923907614692
Epoch: Iteration #400 error is: 0.250955049627593
Epoch: Iteration #500 error is: 0.250824058155342
Epoch: Iteration #600 error is: 0.250823996726474
Epoch: Iteration #700 error is: 0.250823929183869
Epoch: Iteration #800 error is: 0.250823875442116
Epoch: Iteration #900 error is: 0.250823842735095
Epoch: Iteration #1000 error is: 0.250823825500193
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 7.98075544001903
Epoch: Iteration #200 error is: 0.255019681570396
Epoch: Iteration #300 error is: 0.251933394133807
Epoch: Iteration #400 error is: 0.251929656614311
Epoch: Iteration #500 error is: 0.251929648000641
Epoch: Iteration #600 error is: 0.251929642127963
Epoch: Iteration #700 error is: 0.251929632398579
Epoch: Iteration #800 error is: 0.251929618834724
Epoch: Iteration #900 error is: 0.251929601403264
Epoch: Iteration #1000 error is: 0.25192958004361


RUNIT TEST PROTOCOL -- Tue Mar  2 20:28:41 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 
 14.325   1.761  16.069 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.0470.3040.352
birewire.analysis.dsg0.0360.0000.036
birewire.analysis.undirected59.822 0.14159.967
birewire.bipartite.from.incidence0.0010.0270.029
birewire.build.dsg0.0070.0000.007
birewire.induced.bipartite0.0030.0000.002
birewire.rewire.bipartite0.0010.0270.028
birewire.rewire.bipartite.and.projections0.0620.0030.066
birewire.rewire.dsg0.0030.0010.003
birewire.rewire.undirected0.4770.0430.520
birewire.similarity0.1460.0000.147
birewire.similarity.dsg0.0180.0000.018
birewire.visual.monitoring.bipartite3.9250.0313.956
birewire.visual.monitoring.dsg23.854 0.01323.878
birewire.visual.monitoring.undirected8.6120.0598.672