Bioconductor Package Maintainer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/graph |
| Branch: RELEASE_3_8 |
| Last Commit: e2aecb0 |
| Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:59 -0400 (Tue, 16 Apr 2019).
| Package 678/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| graph 1.60.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: graph |
| Version: 1.60.0 |
| 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_1.60.0.tar.gz |
| StartedAt: 2019-04-16 00:24:05 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:25:17 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 72.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/graph.Rcheck’ * using R version 3.5.3 (2019-03-11) * 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 ‘1.60.0’ * 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 ‘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. * 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 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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("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 Apr 16 00:25:08 2019
***********************************************
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
5.586 0.151 5.780
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.039 | 0.005 | 0.045 | |
| IMCA | 0.167 | 0.022 | 0.191 | |
| MAPKsig | 0.117 | 0.004 | 0.120 | |
| MultiGraph-class | 0.195 | 0.003 | 0.199 | |
| acc-methods | 0.012 | 0.000 | 0.012 | |
| addEdge | 0.057 | 0.001 | 0.062 | |
| addNode | 0.012 | 0.001 | 0.012 | |
| adj-methods | 0.004 | 0.000 | 0.003 | |
| adjacencyMatrix | 0.004 | 0.001 | 0.004 | |
| apoptosisGraph | 0.014 | 0.001 | 0.015 | |
| attrData-class | 0.000 | 0.000 | 0.001 | |
| aveNumEdges | 0.004 | 0.000 | 0.003 | |
| biocRepos | 0.002 | 0.001 | 0.003 | |
| boundary | 0.003 | 0.000 | 0.003 | |
| calcProb | 0.000 | 0.000 | 0.001 | |
| calcSumProb | 0.005 | 0.001 | 0.006 | |
| clearNode | 0.016 | 0.001 | 0.017 | |
| clusterGraph-class | 0.017 | 0.000 | 0.017 | |
| clusteringCoefficient-methods | 0.037 | 0.001 | 0.037 | |
| combineNodes | 0.092 | 0.000 | 0.095 | |
| distGraph-class | 0.001 | 0.000 | 0.001 | |
| duplicatedEdges | 0 | 0 | 0 | |
| edgeMatrix | 0.007 | 0.001 | 0.008 | |
| edgeSets | 0.033 | 0.006 | 0.039 | |
| edgeWeights | 0.007 | 0.000 | 0.008 | |
| fromGXL-methods | 0.241 | 0.007 | 0.253 | |
| graph-class | 0.003 | 0.001 | 0.004 | |
| graph2SparseM | 0.100 | 0.003 | 0.106 | |
| graphAM-class | 0.008 | 0.000 | 0.009 | |
| graphBAM-class | 0.026 | 0.001 | 0.027 | |
| graphExamples | 0.005 | 0.002 | 0.006 | |
| graphNEL-class | 0.009 | 0.000 | 0.010 | |
| inEdges | 0.006 | 0.000 | 0.006 | |
| leaves | 0.008 | 0.002 | 0.009 | |
| listEdges | 0.016 | 0.001 | 0.017 | |
| matrix2Graph | 0.025 | 0.001 | 0.027 | |
| mostEdges | 0.007 | 0.001 | 0.006 | |
| numNoEdges | 0.003 | 0.000 | 0.003 | |
| pancrCaIni | 0.170 | 0.003 | 0.174 | |
| randomEGraph | 0.007 | 0.000 | 0.007 | |
| randomGraph | 0.003 | 0.000 | 0.004 | |
| randomNodeGraph | 0.004 | 0.000 | 0.004 | |
| removeEdge | 0.017 | 0.000 | 0.018 | |
| removeNode | 0.008 | 0.000 | 0.008 | |
| renderInfo-class | 0.008 | 0.001 | 0.010 | |
| reverseEdgeDirections | 0.006 | 0.000 | 0.006 | |
| simpleEdge-class | 0.001 | 0.000 | 0.002 | |
| standardLabeling | 0.053 | 0.002 | 0.058 | |
| subGraph | 0.002 | 0.000 | 0.003 | |
| toDotR-methods | 0.026 | 0.003 | 0.034 | |
| ugraph | 0.015 | 0.000 | 0.016 | |
| validGraph | 0.003 | 0.000 | 0.004 | |