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CHECK report for RBGL on celaya2

This page was generated on 2019-04-09 12:47:41 -0400 (Tue, 09 Apr 2019).

Package 1289/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.59.5
Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RBGL
Branch: master
Last Commit: c16aa45
Last Changed Date: 2019-03-28 16:31:49 -0400 (Thu, 28 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: RBGL
Version: 1.59.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RBGL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RBGL_1.59.5.tar.gz
StartedAt: 2019-04-09 04:46:22 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:47:19 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 56.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RBGL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RBGL_1.59.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RBGL.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.59.5’
* 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 ‘RBGL’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RBGL/libs/RBGL.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.9-bioc/meat/RBGL.Rcheck/00check.log’
for details.

Installation output

RBGL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RBGL
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c cliques.cpp -o cliques.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c clusteringCoef.cpp -o clusteringCoef.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c dominatorTree.cpp -o dominatorTree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.cpp:3:
In file included from ./edmonds_optimum_branching.hpp:94:
./edmonds_optimum_branching_impl.hpp:520:71: warning: unused typedef 'EdgeIter' [-Wunused-local-typedef]
    typedef typename graph_traits<TEdgeListGraph>::edge_iterator      EdgeIter;
                                                                      ^
./edmonds_optimum_branching_impl.hpp:521:71: warning: unused typedef 'weight_t' [-Wunused-local-typedef]
    typedef typename property_traits<TWeightMap>::value_type          weight_t;
                                                                      ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c hcs.cpp -o hcs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
            BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
                                      ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c interfaces.cpp -o interfaces.o
interfaces.cpp:57:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef]
        typedef property_map<Graph_dd, vertex_color_t>::type Color;
                                                             ^
interfaces.cpp:98:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:99:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:143:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:142:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:198:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:199:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:225:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:226:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:253:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:252:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:295:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:320:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
interfaces.cpp:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
16 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c minST.cpp -o minST.o
minST.cpp:14:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
minST.cpp:48:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
minST.cpp:81:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c mincut.cpp -o mincut.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c ordering.cpp -o ordering.o
ordering.cpp:182:48: warning: unused variable 'id' [-Wunused-variable]
                property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g);
                                                             ^
ordering.cpp:133:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
                typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                                  ^
ordering.cpp:176:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
                typedef graph_traits<Graph_dd>::vertex_descriptor Vertex;
                                                                  ^
ordering.cpp:232:47: warning: unused typedef 'Pair' [-Wunused-local-typedef]
                typedef std::pair<std::size_t, std::size_t> Pair;
                                                            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c planar.cpp -o planar.o
planar.cpp:225:34: warning: unused variable 'oi_end' [-Wunused-variable]
           Vertex_Vec_t::iterator oi, oi_end = ordering.end();
                                      ^
planar.cpp:429:36: warning: unused variable 'ki_end' [-Wunused-variable]
           Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end();
                                    ^
planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable]
        int i, j = 0;
            ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c registerSigHandlers.cpp -o registerSigHandlers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp:17:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
shortestPath.cpp:136:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
shortestPath.cpp:180:39: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef std::pair < int, int >Edge;
                                      ^
shortestPath.cpp:177:81: warning: unused typedef 'Graph' [-Wunused-local-typedef]
        property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
                                                                                ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c sna.cpp -o sna.o
sna.cpp:161:9: warning: unused variable 'res_cap' [-Wunused-variable]
        res_cap = get(edge_residual_capacity, flow_g);
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c transitive_closure.cpp -o transitive_closure.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c wavefront.cpp -o wavefront.o
clang++ -std=gnu++11 -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 RBGL.so cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-RBGL/00new/RBGL/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RBGL.Rnw’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RBGL)

Tests output

RBGL.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("RBGL")

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 04:47:10 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RBGL RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.953   0.175   1.075

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.7000.0830.784
astarSearch0.0550.0000.069
bandwidth0.0110.0000.012
bellman.ford.sp0.0670.0030.070
bfs0.0150.0020.017
biConnComp0.0060.0010.008
boyerMyrvoldPlanarityTest0.0100.0010.014
chrobakPayneStraightLineDrawing0.0480.0030.053
clusteringCoef0.0150.0010.016
clusteringCoefAppr0.0090.0000.010
coloring0.0080.0010.008
connectedComp0.0150.0020.019
dag.sp0.0110.0020.012
dijkstra.sp0.0290.0030.034
dominatorTree0.0080.0010.010
edgeConn0.0110.0010.012
edmondsMaxCardinalityMatching0.0180.0020.022
edmondsOptimumBranching0.0060.0000.007
extractPath0.0040.0020.006
floyd.warshall.all.pairs.sp0.0050.0010.006
gprofile0.0040.0010.005
graphGenerator0.0010.0000.001
highlyConnSG0.0090.0000.009
incrConnComp0.0070.0010.008
is.triangulated0.0130.0010.014
isKuratowskiSubgraph0.0160.0010.019
isStraightLineDrawing0.010.000.01
isomorphism0.0150.0010.016
johnson.all.pairs.sp0.0090.0010.011
kCliques0.0060.0010.007
kCores0.0450.0020.047
lambdaSets0.0110.0020.014
layout000
makeBiconnectedPlanar0.0130.0010.014
makeConnected0.0070.0010.008
makeMaximalPlanar0.0120.0010.013
maxClique0.0140.0020.016
maxFlow0.0160.0000.017
minCut0.0050.0000.005
mstree.kruskal0.0250.0020.027
mstree.prim0.0100.0020.011
ordering0.0130.0020.015
planarCanonicalOrdering0.0080.0010.009
planarFaceTraversal0.0090.0010.010
removeSelfLoops0.0130.0010.014
separates0.0160.0010.016
sp.between0.0340.0040.037
strongComp0.0150.0010.016
transClosure0.0200.0020.021
transitivity0.0080.0010.008
tsort0.0060.0040.010
wavefront0.0050.0010.006