Multiple platform build/check report for BioC 3.14 - CHECK results for graph on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: graph

Version: 1.72.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings graph_1.72.0.tar.gz

StartedAt: 2022-04-12 20:47:49 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:49:22 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 93.4 seconds

RetCode: 0

Status: OK

CheckDir: graph.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings graph_1.72.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.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 'graph/DESCRIPTION' ... OK
* this is package 'graph' version '1.72.0'
* 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 '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.
* 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 use of PKG_*FLAGS in Makefiles ... 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-3.14-bioc/R/library/graph/libs/i386/BioC_graph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/graph/libs/x64/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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/graph_1.72.0.tar.gz && rm -rf graph.buildbin-libdir && mkdir graph.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graph.buildbin-libdir graph_1.72.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL graph_1.72.0.zip && rm graph_1.72.0.tar.gz graph_1.72.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  327k  100  327k    0     0   454k      0 --:--:-- --:--:-- --:--:--  454k

install for i386

* installing *source* package 'graph' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
C:/rtools40/mingw32/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-3~1.14-/R/bin/i386 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/multiGraph-class.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/show+2CmultiGraph-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/isDirected+2CmultiGraph-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/nodes+2CmultiGraph-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/numNodes+2CmultiGraph-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/edges+2CmultiGraph-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/help/numEdges+2CmultiGraph-method.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 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 'graph' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
C:/rtools40/mingw64/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-3~1.14-/R/bin/x64 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/graph.buildbin-libdir/graph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graph' as graph_1.72.0.zip
* DONE (graph)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'graph' successfully unpacked and MD5 sums checked


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.

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

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



RUNIT TEST PROTOCOL -- Tue Apr 12 20:49:05 2022 
*********************************************** 
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 208 test functions, 0 errors, 0 failures
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.42    0.07    4.61


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.

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

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



RUNIT TEST PROTOCOL -- Tue Apr 12 20:49:10 2022 
*********************************************** 
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 208 test functions, 0 errors, 0 failures
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.34    0.14    4.45

name	user	system	elapsed
DFS	0.03	0.00	0.04
IMCA	0.14	0.02	0.15
MAPKsig	0.11	0.00	0.11
MultiGraph-class	0.12	0.01	0.14
acc-methods	0	0	0
addEdge	0.05	0.00	0.04
addNode	0	0	0
adj-methods	0	0	0
adjacencyMatrix	0.01	0.00	0.02
apoptosisGraph	0.00	0.02	0.02
attrData-class	0.02	0.00	0.01
aveNumEdges	0	0	0
biocRepos	0	0	0
boundary	0	0	0
calcProb	0	0	0
calcSumProb	0.02	0.00	0.01
clearNode	0.02	0.00	0.02
clusterGraph-class	0.01	0.00	0.01
clusteringCoefficient-methods	0.03	0.00	0.03
combineNodes	0.11	0.00	0.11
distGraph-class	0	0	0
duplicatedEdges	0	0	0
edgeMatrix	0.01	0.00	0.02
edgeSets	0.07	0.00	0.06
edgeWeights	0.01	0.00	0.01
fromGXL-methods	0.22	0.00	0.22
graph-class	0.02	0.00	0.02
graph2SparseM	0.09	0.00	0.09
graphAM-class	0	0	0
graphBAM-class	0.04	0.00	0.03
graphExamples	0	0	0
graphNEL-class	0.01	0.00	0.01
inEdges	0	0	0
leaves	0.00	0.01	0.02
listEdges	0.02	0.00	0.02
matrix2Graph	0.01	0.00	0.01
mostEdges	0.02	0.00	0.02
numNoEdges	0	0	0
pancrCaIni	0.17	0.00	0.17
randomEGraph	0	0	0
randomGraph	0	0	0
randomNodeGraph	0.02	0.00	0.01
removeEdge	0	0	0
removeNode	0	0	0
renderInfo-class	0.01	0.00	0.02
reverseEdgeDirections	0	0	0
simpleEdge-class	0	0	0
standardLabeling	0.06	0.00	0.06
subGraph	0	0	0
toDotR-methods	0.02	0.00	0.02
ugraph	0.02	0.00	0.01
validGraph	0	0	0

name	user	system	elapsed
DFS	0.03	0.00	0.03
IMCA	0.13	0.04	0.15
MAPKsig	0.13	0.00	0.12
MultiGraph-class	0.12	0.00	0.13
acc-methods	0.02	0.00	0.02
addEdge	0.03	0.00	0.03
addNode	0.02	0.00	0.01
adj-methods	0	0	0
adjacencyMatrix	0	0	0
apoptosisGraph	0.01	0.00	0.02
attrData-class	0	0	0
aveNumEdges	0	0	0
biocRepos	0	0	0
boundary	0	0	0
calcProb	0	0	0
calcSumProb	0	0	0
clearNode	0.02	0.00	0.01
clusterGraph-class	0.02	0.00	0.02
clusteringCoefficient-methods	0.03	0.00	0.03
combineNodes	0.07	0.00	0.08
distGraph-class	0	0	0
duplicatedEdges	0	0	0
edgeMatrix	0	0	0
edgeSets	0.05	0.00	0.05
edgeWeights	0	0	0
fromGXL-methods	0.17	0.00	0.19
graph-class	0.01	0.00	0.02
graph2SparseM	0.10	0.00	0.09
graphAM-class	0	0	0
graphBAM-class	0.03	0.00	0.03
graphExamples	0	0	0
graphNEL-class	0.02	0.00	0.02
inEdges	0	0	0
leaves	0.01	0.00	0.01
listEdges	0.02	0.00	0.02
matrix2Graph	0.01	0.00	0.01
mostEdges	0	0	0
numNoEdges	0	0	0
pancrCaIni	0.17	0.01	0.19
randomEGraph	0	0	0
randomGraph	0.02	0.00	0.02
randomNodeGraph	0	0	0
removeEdge	0	0	0
removeNode	0.02	0.00	0.01
renderInfo-class	0	0	0
reverseEdgeDirections	0	0	0
simpleEdge-class	0	0	0
standardLabeling	0.04	0.02	0.06
subGraph	0	0	0
toDotR-methods	0.02	0.00	0.02
ugraph	0	0	0
validGraph	0	0	0

CHECK results for graph on tokay2

Summary

Command output

Installation output

Tests output

Example timings