Package: hyperdraw

Version: 1.34.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:hyperdraw.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings hyperdraw_1.34.0.tar.gz

StartedAt: 2019-04-16 00:41:40 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:42:15 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 34.9 seconds

RetCode: 0

Status:  OK

CheckDir: hyperdraw.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:hyperdraw.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings hyperdraw_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/hyperdraw.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hyperdraw/DESCRIPTION’ ... OK
* this is package ‘hyperdraw’ version ‘1.34.0’
* 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 ‘hyperdraw’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL hyperdraw
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘hyperdraw’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graphLayout’ in package ‘hyperdraw’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hyperdraw)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> 
> library(hyperdraw)
> 
> # Check graph validation
> 
> # Edges must be directed
> 
> badgnel.1 <- new("graphNEL",
+                 nodes=c("A", "R"),
+                 edgeL=list(
+                   A=list(edges="R"),
+                   R=list(edges="A")))
> stopifnot(inherits(try(graphBPH(badgnel.1, "")), "try-error"))
Error in validGraphBPH(.Object) : 
  All edges must be between a normal node and an edge node
> 
> # All edges must be between normal node and edge node
> badgnel.2 <- new("graphNEL",
+                  nodes=c("A", "B"),
+                  edgeL=list(
+                    A=list(edges="B"),
+                    B=list(edges="A")),
+                  edgemode="directed")
> stopifnot(inherits(try(graphBPH(badgnel.2, "")), "try-error"))
Error in validGraphBPH(.Object) : 
  All edges must be between a normal node and an edge node
> 
> # If it's a Hypergraph, all Hyperedges must be DirectedHyperedges
> 
> require(hypergraph)
Loading required package: hypergraph
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

> 
> badhg <- Hypergraph(c("A", "B"), list(Hyperedge(c("A", "B"))))
> stopifnot(inherits(try(graphBPH(badhg)), "try-error"))
Error in graphBPH(badhg) : All hyperedges must be directed hyperedges
> 
> # Examples in man pages test simple examples that should work
> 
> 
> proc.time()
   user  system elapsed 
  1.212   0.040   1.262 

name	user	system	elapsed
RagraphBPH-class	0.816	0.004	0.856
graphBPH-class	0.584	0.000	0.617
graphLayout	0.008	0.000	0.010