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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:hyperdraw.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hyperdraw_1.61.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/hyperdraw.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hyperdraw/DESCRIPTION’ ... OK
* this is package ‘hyperdraw’ version ‘1.61.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RagraphBPH-class.Rd: Ragraph-class
  graphBPH-class.Rd: agopen, graphNEL-class
  graphLayout.Rd: agopen, GraphvizLayouts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/hyperdraw.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL hyperdraw
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘hyperdraw’ ...
** this is package ‘hyperdraw’ version ‘1.61.0’
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hyperdraw)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, 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 
  1.018   0.078   1.085