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CHECK report for RBGL on machv2

This page was generated on 2020-10-17 11:59:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RBGL PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1421/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.64.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RBGL
Branch: RELEASE_3_11
Last Commit: 2f5aeaf
Last Changed Date: 2020-04-27 14:08:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RBGL
Version: 1.64.0
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_1.64.0.tar.gz
StartedAt: 2020-10-17 04:22:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:23:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 57.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RBGL.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.64.0’
* 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 ‘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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/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-3.11-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/4.0/Resources/library’
* installing *source* package ‘RBGL’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bbc.cpp -o bbc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cliques.cpp -o cliques.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c clusteringCoef.cpp -o clusteringCoef.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c dominatorTree.cpp -o dominatorTree.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hcs.cpp -o hcs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c interfaces.cpp -o interfaces.o
interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef]
        typedef property_map<Graph_dd, vertex_color_t>::type Color;
                                                             ^
interfaces.cpp:57:60: 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:98:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:142:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:143:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
                                                             ^
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:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::edge_descriptor Edge;
                                                           ^
interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
        typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
                                                             ^
16 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c mincut.cpp -o mincut.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerSigHandlers.cpp -o registerSigHandlers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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:177:81: warning: unused typedef 'Graph' [-Wunused-local-typedef]
        property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
                                                                                ^
shortestPath.cpp:180:39: warning: unused typedef 'Edge' [-Wunused-local-typedef]
        typedef std::pair < int, int >Edge;
                                      ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c transitive_closure.cpp -o transitive_closure.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c wavefront.cpp -o wavefront.o
clang++ -mmacosx-version-min=10.13 -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 bbc.o 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/4.0/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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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, which.max, which.min



RUNIT TEST PROTOCOL -- Sat Oct 17 04:22:47 2020 
*********************************************** 
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 
  1.086   0.101   1.165 

Example timings

RBGL.Rcheck/RBGL-Ex.timings

nameusersystemelapsed
FileDep0.5920.0380.631
astarSearch0.0690.0000.070
bandwidth0.0110.0000.011
bellman.ford.sp0.0370.0020.039
bfs0.0110.0010.011
biConnComp0.0080.0010.009
boyerMyrvoldPlanarityTest0.0100.0010.011
chrobakPayneStraightLineDrawing0.0440.0020.046
clusteringCoef0.0110.0010.012
clusteringCoefAppr0.0060.0010.007
coloring0.0060.0010.007
connectedComp0.0140.0010.016
dag.sp0.0090.0020.010
dijkstra.sp0.0210.0030.025
dominatorTree0.0070.0010.008
edgeConn0.0050.0010.006
edmondsMaxCardinalityMatching0.0110.0020.013
edmondsOptimumBranching0.0080.0010.009
extractPath0.0040.0020.006
floyd.warshall.all.pairs.sp0.0080.0010.010
gprofile0.0070.0010.008
graphGenerator0.0010.0010.001
highlyConnSG0.0090.0010.010
incrConnComp0.0070.0010.008
is.triangulated0.0090.0010.010
isKuratowskiSubgraph0.0100.0020.011
isStraightLineDrawing0.0080.0010.009
isomorphism0.0120.0020.013
johnson.all.pairs.sp0.0080.0020.008
kCliques0.0070.0020.009
kCores0.0460.0030.049
lambdaSets0.0110.0010.012
layout0.0000.0000.001
makeBiconnectedPlanar0.0110.0010.011
makeConnected0.0090.0000.010
makeMaximalPlanar0.0110.0010.012
maxClique0.0130.0010.014
maxFlow0.0110.0010.013
minCut0.0070.0010.009
mstree.kruskal0.0230.0020.026
mstree.prim0.0080.0010.008
ordering0.0100.0020.012
planarCanonicalOrdering0.0090.0010.010
planarFaceTraversal0.0130.0010.015
removeSelfLoops0.0120.0010.012
separates0.0130.0010.015
sp.between0.0280.0030.032
strongComp0.0120.0010.013
transClosure0.010.000.01
transitivity0.0070.0000.007
tsort0.0050.0020.007
wavefront0.0070.0000.008