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CHECK report for BiRewire on merida1

This page was generated on 2019-04-16 11:57:08 -0400 (Tue, 16 Apr 2019).

Package 163/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.14.0
Andrea Gobbi
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: RELEASE_3_8
Last Commit: f0cbc88
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.14.0
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_3.14.0.tar.gz
StartedAt: 2019-04-15 22:39:17 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:43:16 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 239.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BiRewire.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.14.0’
* 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 ... 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
  ‘plot’
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 ‘plot’
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
  ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 plot polygon qt
  read.table sd text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "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 or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          73.706  0.235  74.924
birewire.visual.monitoring.dsg        51.956  0.406  52.818
birewire.visual.monitoring.undirected 15.678  1.261  17.084
birewire.visual.monitoring.bipartite   8.585  0.074   8.737
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-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
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BiRewire’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interface.c -o interface.o
clang -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/3.5/Resources/library/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
* DONE (BiRewire)

Tests output

BiRewire.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 9.96923258158518
Epoch: Iteration #200 error is: 0.554942010324235
Epoch: Iteration #300 error is: 0.312815191160684
Epoch: Iteration #400 error is: 0.272301505450023
Epoch: Iteration #500 error is: 0.264939527663983
Epoch: Iteration #600 error is: 0.259101764451265
Epoch: Iteration #700 error is: 0.254883007983713
Epoch: Iteration #800 error is: 0.253690333152106
Epoch: Iteration #900 error is: 0.253183594854582
Epoch: Iteration #1000 error is: 0.252650462915133
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.6866130237136
Epoch: Iteration #200 error is: 0.440535347793367
Epoch: Iteration #300 error is: 0.289882730729361
Epoch: Iteration #400 error is: 0.258493344130986
Epoch: Iteration #500 error is: 0.252480260598687
Epoch: Iteration #600 error is: 0.251856391470945
Epoch: Iteration #700 error is: 0.251438154291587
Epoch: Iteration #800 error is: 0.25106080580424
Epoch: Iteration #900 error is: 0.250875915542724
Epoch: Iteration #1000 error is: 0.250836856475931
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.20319084703243
Epoch: Iteration #200 error is: 0.273884902241017
Epoch: Iteration #300 error is: 0.252459168323227
Epoch: Iteration #400 error is: 0.251238677226972
Epoch: Iteration #500 error is: 0.250833741037143
Epoch: Iteration #600 error is: 0.250831636362507
Epoch: Iteration #700 error is: 0.250831626754836
Epoch: Iteration #800 error is: 0.25083161028893
Epoch: Iteration #900 error is: 0.250831580454071
Epoch: Iteration #1000 error is: 0.250831527138279
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.3789532377753
Epoch: Iteration #200 error is: 0.357065493660464
Epoch: Iteration #300 error is: 0.253825517578298
Epoch: Iteration #400 error is: 0.251342809632496
Epoch: Iteration #500 error is: 0.250960744317454
Epoch: Iteration #600 error is: 0.250843001303121
Epoch: Iteration #700 error is: 0.250829613861035
Epoch: Iteration #800 error is: 0.250828988575461
Epoch: Iteration #900 error is: 0.250828939521479
Epoch: Iteration #1000 error is: 0.250828897572218
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 16.4143934908346
Epoch: Iteration #200 error is: 0.332947897389945
Epoch: Iteration #300 error is: 0.259650859679855
Epoch: Iteration #400 error is: 0.252258511829265
Epoch: Iteration #500 error is: 0.251228656417871
Epoch: Iteration #600 error is: 0.250856243108417
Epoch: Iteration #700 error is: 0.250833370620112
Epoch: Iteration #800 error is: 0.250833086168338
Epoch: Iteration #900 error is: 0.250833077043229
Epoch: Iteration #1000 error is: 0.250833066349824
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 21.6295832823988
Epoch: Iteration #200 error is: 0.419077459974383
Epoch: Iteration #300 error is: 0.275123146198147
Epoch: Iteration #400 error is: 0.263952636862259
Epoch: Iteration #500 error is: 0.260158935862751
Epoch: Iteration #600 error is: 0.258278196102054
Epoch: Iteration #700 error is: 0.25613269858226
Epoch: Iteration #800 error is: 0.254021149027658
Epoch: Iteration #900 error is: 0.252778376021993
Epoch: Iteration #1000 error is: 0.251714265455263
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 9.48067054969474
Epoch: Iteration #200 error is: 0.30271796482119
Epoch: Iteration #300 error is: 0.252198344248849
Epoch: Iteration #400 error is: 0.250869520261568
Epoch: Iteration #500 error is: 0.250831148603413
Epoch: Iteration #600 error is: 0.25083103669113
Epoch: Iteration #700 error is: 0.25083090028431
Epoch: Iteration #800 error is: 0.250830667032919
Epoch: Iteration #900 error is: 0.250830288357932
Epoch: Iteration #1000 error is: 0.25082971065172
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 17.3588000400004
Epoch: Iteration #200 error is: 0.378556188331296
Epoch: Iteration #300 error is: 0.291821716312798
Epoch: Iteration #400 error is: 0.280191233972252
Epoch: Iteration #500 error is: 0.266583208639847
Epoch: Iteration #600 error is: 0.256793173215814
Epoch: Iteration #700 error is: 0.254124639846868
Epoch: Iteration #800 error is: 0.253130554486492
Epoch: Iteration #900 error is: 0.252538196425121
Epoch: Iteration #1000 error is: 0.252272543821238


RUNIT TEST PROTOCOL -- Mon Apr 15 22:43:11 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
 26.254   1.369  27.835 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1920.1690.366
birewire.analysis.dsg0.0870.0140.100
birewire.analysis.undirected73.706 0.23574.924
birewire.bipartite.from.incidence0.0110.0130.024
birewire.build.dsg0.0080.0010.010
birewire.induced.bipartite0.0030.0010.004
birewire.rewire.bipartite0.0120.0180.030
birewire.rewire.bipartite.and.projections0.1660.0080.175
birewire.rewire.dsg0.0060.0010.007
birewire.rewire.undirected1.0160.0551.081
birewire.similarity0.0080.0010.009
birewire.similarity.dsg0.0260.0020.028
birewire.visual.monitoring.bipartite8.5850.0748.737
birewire.visual.monitoring.dsg51.956 0.40652.818
birewire.visual.monitoring.undirected15.678 1.26117.084