Package: graph

Version: 1.61.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graph_1.61.1.tar.gz

StartedAt: 2019-04-09 01:21:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:22:14 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 67.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: graph.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graph_1.61.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/graph.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.61.1’
* 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 ‘graph’ 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 ... NOTE
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... 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 ... ERROR
Running examples in ‘graph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: removeEdge
> ### Title: removeEdge
> ### Aliases: removeEdge
> ### Keywords: manip
> 
> ### ** Examples
> 
>   V <- LETTERS[1:4]
>   edL1 <- vector("list", length=4)
>   names(edL1) <- V
>   for(i in 1:4)
+     edL1[[i]] <- list(edges=c(2,1,4,3)[i], weights=sqrt(i))
>   gR <- graphNEL(nodes=V, edgeL=edL1)
> 
>   gX <- removeEdge("A", "B", gR)
> 
>   set.seed(123)
>   g <- randomEGraph(V=letters[1:5],edges=5)
>   g2 <- removeEdge(from=c("a","b"), to=c("c","e"), g)
Error in .verifyEdges(graph, from, to) : edges not found: ‘a|c, c|a’
Calls: removeEdge ... removeEdge -> clearEdgeData -> .getEdgeKeys -> .verifyEdges
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/graph.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graph
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘graph’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c graph.c -o graph.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 graph.so graph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv graph.so BioC_graph.so
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/graph/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 (graph)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("graph", pattern="_test.R")

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, 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



RUNIT TEST PROTOCOL -- Tue Apr  9 01:22:04 2019 
*********************************************** 
Number of test functions: 206 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 206 test functions, 0 errors, 0 failures
Number of test functions: 206 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.106   0.161   5.278 

name	user	system	elapsed
DFS	0.034	0.005	0.040
IMCA	0.151	0.022	0.173
MAPKsig	0.126	0.002	0.130
MultiGraph-class	0.178	0.003	0.181
acc-methods	0.009	0.000	0.010
addEdge	0.047	0.001	0.047
addNode	0.01	0.00	0.01
adj-methods	0.004	0.000	0.004
adjacencyMatrix	0.002	0.000	0.002
apoptosisGraph	0.020	0.002	0.022
attrData-class	0.001	0.000	0.002
aveNumEdges	0.004	0.000	0.004
biocRepos	0.002	0.001	0.003
boundary	0.003	0.000	0.004
calcProb	0.001	0.000	0.000
calcSumProb	0.006	0.000	0.006
clearNode	0.015	0.001	0.015
clusterGraph-class	0.012	0.000	0.012
clusteringCoefficient-methods	0.035	0.000	0.037
combineNodes	0.103	0.001	0.104
distGraph-class	0.001	0.001	0.001
duplicatedEdges	0.001	0.000	0.000
edgeMatrix	0.007	0.000	0.008
edgeSets	0.033	0.005	0.037
edgeWeights	0.008	0.000	0.008
fromGXL-methods	0.191	0.007	0.199
graph-class	0.005	0.000	0.005
graph2SparseM	0.114	0.005	0.119
graphAM-class	0.022	0.001	0.022
graphBAM-class	0.025	0.001	0.026
graphExamples	0.004	0.001	0.006
graphNEL-class	0.008	0.000	0.008
inEdges	0.005	0.000	0.006
leaves	0.012	0.002	0.014
listEdges	0.013	0.002	0.014
matrix2Graph	0.023	0.001	0.024
mostEdges	0.010	0.000	0.011
numNoEdges	0.004	0.001	0.005
pancrCaIni	0.195	0.003	0.200
randomEGraph	0.006	0.000	0.006
randomGraph	0.003	0.000	0.004
randomNodeGraph	0.003	0.000	0.002