Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/graph |
| Branch: RELEASE_3_10 |
| Last Commit: 3d35921 |
| Last Changed Date: 2019-10-29 13:07:23 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:04:00 -0400 (Wed, 15 Apr 2020).
| Package 740/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| graph 1.64.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: graph |
| Version: 1.64.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings graph_1.64.0.tar.gz |
| StartedAt: 2020-04-15 00:09:12 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:10:13 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 61.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: graph.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings graph_1.64.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/graph.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graph/DESCRIPTION’ ... OK * this is package ‘graph’ 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 ‘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 ... WARNING Documented arguments not in \usage in documentation object 'edgeMatrix': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.10-bioc/meat/graph.Rcheck/00check.log’ for details.
graph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL graph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘graph’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR mv graph.so BioC_graph.so installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-graph/00new/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 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 (graph)
graph.Rcheck/tests/graph_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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 -- Wed Apr 15 00:10:06 2020
***********************************************
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
5.368 0.084 5.503
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.044 | 0.000 | 0.047 | |
| IMCA | 0.184 | 0.008 | 0.193 | |
| MAPKsig | 0.168 | 0.004 | 0.171 | |
| MultiGraph-class | 0.220 | 0.008 | 0.226 | |
| acc-methods | 0.012 | 0.000 | 0.012 | |
| addEdge | 0.072 | 0.000 | 0.071 | |
| addNode | 0.012 | 0.000 | 0.011 | |
| adj-methods | 0.004 | 0.000 | 0.003 | |
| adjacencyMatrix | 0.004 | 0.000 | 0.004 | |
| apoptosisGraph | 0.020 | 0.000 | 0.018 | |
| attrData-class | 0.000 | 0.000 | 0.001 | |
| aveNumEdges | 0.004 | 0.000 | 0.005 | |
| biocRepos | 0.004 | 0.000 | 0.002 | |
| boundary | 0.004 | 0.000 | 0.005 | |
| calcProb | 0 | 0 | 0 | |
| calcSumProb | 0.004 | 0.000 | 0.005 | |
| clearNode | 0.020 | 0.000 | 0.019 | |
| clusterGraph-class | 0.012 | 0.000 | 0.013 | |
| clusteringCoefficient-methods | 0.048 | 0.000 | 0.045 | |
| combineNodes | 0.068 | 0.000 | 0.069 | |
| distGraph-class | 0.000 | 0.000 | 0.001 | |
| duplicatedEdges | 0.004 | 0.000 | 0.000 | |
| edgeMatrix | 0.004 | 0.000 | 0.006 | |
| edgeSets | 0.028 | 0.004 | 0.031 | |
| edgeWeights | 0.008 | 0.000 | 0.007 | |
| fromGXL-methods | 0.164 | 0.008 | 0.359 | |
| graph-class | 0.000 | 0.000 | 0.003 | |
| graph2SparseM | 0.124 | 0.008 | 0.578 | |
| graphAM-class | 0.024 | 0.000 | 0.023 | |
| graphBAM-class | 0.036 | 0.004 | 0.038 | |
| graphExamples | 0.004 | 0.000 | 0.006 | |
| graphNEL-class | 0.012 | 0.000 | 0.008 | |
| inEdges | 0.008 | 0.000 | 0.009 | |
| leaves | 0.012 | 0.000 | 0.012 | |
| listEdges | 0.012 | 0.000 | 0.014 | |
| matrix2Graph | 0.024 | 0.004 | 0.027 | |
| mostEdges | 0.008 | 0.000 | 0.009 | |
| numNoEdges | 0.004 | 0.000 | 0.003 | |
| pancrCaIni | 0.208 | 0.000 | 0.211 | |
| randomEGraph | 0.004 | 0.000 | 0.005 | |
| randomGraph | 0.004 | 0.000 | 0.004 | |
| randomNodeGraph | 0.004 | 0.000 | 0.004 | |
| removeEdge | 0.012 | 0.000 | 0.012 | |
| removeNode | 0.008 | 0.000 | 0.008 | |
| renderInfo-class | 0.008 | 0.000 | 0.008 | |
| reverseEdgeDirections | 0.008 | 0.000 | 0.012 | |
| simpleEdge-class | 0.000 | 0.000 | 0.001 | |
| standardLabeling | 0.092 | 0.000 | 0.093 | |
| subGraph | 0.000 | 0.000 | 0.001 | |
| toDotR-methods | 0.028 | 0.000 | 0.186 | |
| ugraph | 0.008 | 0.000 | 0.011 | |
| validGraph | 0.000 | 0.000 | 0.001 | |