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CHECK report for graph on tokay2

This page was generated on 2018-10-17 08:31:50 -0400 (Wed, 17 Oct 2018).

Package 644/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.58.2
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/graph
Branch: RELEASE_3_7
Last Commit: 6455d8e
Last Changed Date: 2018-10-09 10:23:05 -0400 (Tue, 09 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graph
Version: 1.58.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings graph_1.58.2.tar.gz
StartedAt: 2018-10-17 02:31:50 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:33:20 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 89.2 seconds
RetCode: 0
Status:  OK  
CheckDir: graph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings graph_1.58.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/graph.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'graph/DESCRIPTION' ... OK
* this is package 'graph' version '1.58.2'
* 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 '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
* 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 ... 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.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mg_validate_node_names: no visible global function definition for
  'head'
MultiDiGraph: no visible global function definition for 'head'
plot,graph-ANY: no visible global function definition for 'getMethod'
show,MultiGraph: no visible global function definition for 'head'
Undefined global functions or variables:
  getMethod head
Consider adding
  importFrom("methods", "getMethod")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/graph/libs/i386/BioC_graph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 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 'graph_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/graph.Rcheck/00check.log'
for details.



Installation output

graph.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/graph_1.58.2.tar.gz && rm -rf graph.buildbin-libdir && mkdir graph.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graph.buildbin-libdir graph_1.58.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL graph_1.58.2.zip && rm graph_1.58.2.tar.gz graph_1.58.2.zip
###
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##############################################################################


  % 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  328k  100  328k    0     0  5251k      0 --:--:-- --:--:-- --:--:-- 5868k

install for i386

* installing *source* package 'graph' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/graph.buildbin-libdir/graph/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'graph'
    finding HTML links ... done
    DFS                                     html  
    IMCA                                    html  
    MAPKsig                                 html  
    MultiGraph-class                        html  
    acc-methods                             html  
    addEdge                                 html  
    addNode                                 html  
    adj-methods                             html  
    adjacencyMatrix                         html  
    apoptosisGraph                          html  
    attrData-class                          html  
    attrDataItem-methods                    html  
    attrDefaults-methods                    html  
    aveNumEdges                             html  
    biocRepos                               html  
    boundary                                html  
    calcProb                                html  
    calcSumProb                             html  
    clearNode                               html  
    clusterGraph-class                      html  
    clusteringCoefficient-methods           html  
    combineNodes                            html  
    defunct                                 html  
    distGraph-class                         html  
    duplicatedEdges                         html  
    edgeData-methods                        html  
    edgeDataDefaults-methods                html  
    edgeMatrix                              html  
    edgeSets                                html  
    edgeWeights                             html  
    fromGXL-methods                         html  
    graph-class                             html  
    graph2SparseM                           html  
    graphAM-class                           html  
    graphBAM-class                          html  
    graphExamples                           html  
    graphNEL-class                          html  
    inEdges                                 html  
    internal                                html  
    isAdjacent-methods                      html  
    isDirected-methods                      html  
    leaves                                  html  
    listEdges                               html  
    matrix2Graph                            html  
    mostEdges                               html  
    multigraph                              html  
    nodeData-methods                        html  
    nodeDataDefaults-methods                html  
    numNoEdges                              html  
    pancrCaIni                              html  
    randomEGraph                            html  
    randomGraph                             html  
    randomNodeGraph                         html  
    removeEdge                              html  
    removeNode                              html  
    renderInfo-class                        html  
    reverseEdgeDirections                   html  
    settings                                html  
    simpleEdge-class                        html  
    standardLabeling                        html  
    subGraph                                html  
    toDotR-methods                          html  
    toDotWithRI                             html  
    ugraph                                  html  
    validGraph                              html  
    write.tlp                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'graph' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/graph.buildbin-libdir/graph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graph' as graph_1.58.2.zip
* DONE (graph)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'graph' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

graph.Rcheck/tests_i386/graph_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> 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, lengths, 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 -- Wed Oct 17 02:33:04 2018 
*********************************************** 
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 
   5.37    0.18    7.03 

graph.Rcheck/tests_x64/graph_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> 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, lengths, 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 -- Wed Oct 17 02:33:10 2018 
*********************************************** 
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 
   5.31    0.10    5.42 

Example timings

graph.Rcheck/examples_i386/graph-Ex.timings

nameusersystemelapsed
DFS0.050.000.04
IMCA0.160.070.22
MAPKsig0.160.010.17
MultiGraph-class0.190.020.20
acc-methods0.010.000.02
addEdge0.070.000.06
addNode0.010.000.02
adj-methods000
adjacencyMatrix0.020.000.01
apoptosisGraph0.010.000.02
attrData-class0.020.000.01
aveNumEdges000
biocRepos0.000.010.02
boundary000
calcProb000
calcSumProb0.010.000.02
clearNode0.020.000.01
clusterGraph-class0.010.000.02
clusteringCoefficient-methods0.050.000.04
combineNodes0.080.000.08
distGraph-class000
duplicatedEdges000
edgeMatrix0.020.000.02
edgeSets0.030.020.04
edgeWeights0.010.000.02
fromGXL-methods0.280.000.39
graph-class0.020.000.02
graph2SparseM0.140.000.14
graphAM-class0.020.000.01
graphBAM-class0.040.000.05
graphExamples0.020.000.01
graphNEL-class0.010.000.02
inEdges0.020.000.02
leaves0.010.000.01
listEdges0.020.000.02
matrix2Graph0.030.000.03
mostEdges0.020.000.01
numNoEdges000
pancrCaIni0.220.000.22
randomEGraph000
randomGraph000
randomNodeGraph000
removeEdge0.010.000.02
removeNode0.020.000.02
renderInfo-class000
reverseEdgeDirections0.010.000.01
simpleEdge-class000
standardLabeling0.110.000.11
subGraph000
toDotR-methods0.050.000.05
ugraph0.020.000.01
validGraph000

graph.Rcheck/examples_x64/graph-Ex.timings

nameusersystemelapsed
DFS0.050.000.05
IMCA0.130.020.14
MAPKsig0.120.000.12
MultiGraph-class0.160.000.16
acc-methods000
addEdge0.040.000.05
addNode0.020.000.01
adj-methods000
adjacencyMatrix000
apoptosisGraph0.010.000.02
attrData-class000
aveNumEdges000
biocRepos000
boundary000
calcProb0.020.000.02
calcSumProb000
clearNode0.010.000.01
clusterGraph-class000
clusteringCoefficient-methods0.030.000.04
combineNodes0.080.000.07
distGraph-class000
duplicatedEdges000
edgeMatrix0.020.000.02
edgeSets0.030.010.05
edgeWeights000
fromGXL-methods0.220.000.29
graph-class0.000.020.02
graph2SparseM0.090.000.09
graphAM-class0.020.000.02
graphBAM-class0.030.000.03
graphExamples0.010.000.01
graphNEL-class000
inEdges0.020.000.02
leaves0.010.000.02
listEdges000
matrix2Graph0.020.000.02
mostEdges000
numNoEdges0.010.000.01
pancrCaIni0.140.000.14
randomEGraph000
randomGraph000
randomNodeGraph000
removeEdge000
removeNode0.010.000.01
renderInfo-class000
reverseEdgeDirections0.020.000.02
simpleEdge-class000
standardLabeling0.060.000.06
subGraph000
toDotR-methods0.030.000.03
ugraph000
validGraph000