Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:43 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hyperdraw on tokay2


To the developers/maintainers of the hyperdraw package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hyperdraw.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 895/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hyperdraw 1.46.0  (landing page)
Paul Murrell
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hyperdraw
git_branch: RELEASE_3_14
git_last_commit: 4d60ce6
git_last_commit_date: 2021-10-26 11:55:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hyperdraw
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hyperdraw.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hyperdraw_1.46.0.tar.gz
StartedAt: 2022-04-12 21:14:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:15:42 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 63.0 seconds
RetCode: 0
Status:   OK  
CheckDir: hyperdraw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hyperdraw.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hyperdraw_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/hyperdraw.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hyperdraw/DESCRIPTION' ... OK
* this is package 'hyperdraw' version '1.46.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  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


Installation output

hyperdraw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hyperdraw_1.46.0.tar.gz && rm -rf hyperdraw.buildbin-libdir && mkdir hyperdraw.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hyperdraw.buildbin-libdir hyperdraw_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hyperdraw_1.46.0.zip && rm hyperdraw_1.46.0.tar.gz hyperdraw_1.46.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 13389  100 13389    0     0  37560      0 --:--:-- --:--:-- --:--:-- 37609

install for i386

* installing *source* package 'hyperdraw' ...
** 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
  converting help for package 'hyperdraw'
    finding HTML links ... done
    RagraphBPH-class                        html  
    finding level-2 HTML links ... done

    graphBPH-class                          html  
    graphBPH                                html  
    graphLayout                             html  
** 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

install for x64

* installing *source* package 'hyperdraw' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hyperdraw' as hyperdraw_1.46.0.zip
* DONE (hyperdraw)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'hyperdraw' successfully unpacked and MD5 sums checked

Tests output

hyperdraw.Rcheck/tests_i386/test.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 
   1.14    0.06    1.18 

hyperdraw.Rcheck/tests_x64/test.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 
   1.17    0.07    1.23 

Example timings

hyperdraw.Rcheck/examples_i386/hyperdraw-Ex.timings

nameusersystemelapsed
RagraphBPH-class0.640.010.66
graphBPH-class0.340.000.35
graphLayout000

hyperdraw.Rcheck/examples_x64/hyperdraw-Ex.timings

nameusersystemelapsed
RagraphBPH-class0.440.000.44
graphBPH-class0.310.000.31
graphLayout000