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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:46:00 -0400 (Wed, 17 Oct 2018).
| Package 644/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| graph 1.58.2 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: graph |
| Version: 1.58.2 |
| 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_1.58.2.tar.gz |
| StartedAt: 2018-10-16 21:50:59 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:52:01 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 62.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
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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_1.58.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/graph.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.58.2’
* 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 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.
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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/graph.Rcheck/00check.log’
for details.
graph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graph ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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/3.5/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)
graph.Rcheck/tests/graph_unit_tests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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 -- Tue Oct 16 21:51:52 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
5.084 0.158 5.254
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.046 | 0.005 | 0.052 | |
| IMCA | 0.143 | 0.021 | 0.164 | |
| MAPKsig | 0.141 | 0.004 | 0.144 | |
| MultiGraph-class | 0.154 | 0.004 | 0.159 | |
| acc-methods | 0.008 | 0.000 | 0.009 | |
| addEdge | 0.038 | 0.001 | 0.038 | |
| addNode | 0.009 | 0.000 | 0.010 | |
| adj-methods | 0.004 | 0.001 | 0.003 | |
| adjacencyMatrix | 0.003 | 0.000 | 0.003 | |
| apoptosisGraph | 0.013 | 0.002 | 0.015 | |
| attrData-class | 0.004 | 0.000 | 0.004 | |
| aveNumEdges | 0.004 | 0.001 | 0.005 | |
| biocRepos | 0.002 | 0.001 | 0.003 | |
| boundary | 0.003 | 0.000 | 0.004 | |
| calcProb | 0.001 | 0.000 | 0.001 | |
| calcSumProb | 0.005 | 0.001 | 0.005 | |
| clearNode | 0.012 | 0.000 | 0.012 | |
| clusterGraph-class | 0.009 | 0.000 | 0.008 | |
| clusteringCoefficient-methods | 0.031 | 0.001 | 0.031 | |
| combineNodes | 0.071 | 0.000 | 0.071 | |
| distGraph-class | 0.004 | 0.001 | 0.004 | |
| duplicatedEdges | 0.001 | 0.000 | 0.001 | |
| edgeMatrix | 0.014 | 0.001 | 0.015 | |
| edgeSets | 0.037 | 0.006 | 0.044 | |
| edgeWeights | 0.011 | 0.000 | 0.012 | |
| fromGXL-methods | 0.177 | 0.008 | 0.186 | |
| graph-class | 0.009 | 0.001 | 0.009 | |
| graph2SparseM | 0.112 | 0.004 | 0.115 | |
| graphAM-class | 0.013 | 0.000 | 0.014 | |
| graphBAM-class | 0.038 | 0.001 | 0.039 | |
| graphExamples | 0.005 | 0.001 | 0.006 | |
| graphNEL-class | 0.008 | 0.000 | 0.009 | |
| inEdges | 0.007 | 0.001 | 0.007 | |
| leaves | 0.014 | 0.001 | 0.016 | |
| listEdges | 0.018 | 0.001 | 0.019 | |
| matrix2Graph | 0.021 | 0.001 | 0.022 | |
| mostEdges | 0.007 | 0.000 | 0.008 | |
| numNoEdges | 0.005 | 0.000 | 0.006 | |
| pancrCaIni | 0.154 | 0.003 | 0.157 | |
| randomEGraph | 0.008 | 0.000 | 0.008 | |
| randomGraph | 0.007 | 0.001 | 0.007 | |
| randomNodeGraph | 0.006 | 0.000 | 0.006 | |
| removeEdge | 0.014 | 0.000 | 0.014 | |
| removeNode | 0.01 | 0.00 | 0.01 | |
| renderInfo-class | 0.011 | 0.000 | 0.012 | |
| reverseEdgeDirections | 0.008 | 0.000 | 0.008 | |
| simpleEdge-class | 0.001 | 0.000 | 0.002 | |
| standardLabeling | 0.051 | 0.001 | 0.051 | |
| subGraph | 0.003 | 0.000 | 0.003 | |
| toDotR-methods | 0.027 | 0.002 | 0.035 | |
| ugraph | 0.012 | 0.000 | 0.012 | |
| validGraph | 0.002 | 0.000 | 0.002 | |