Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/graph |
| Branch: RELEASE_3_6 |
| Last Commit: c4abe22 |
| Last Changed Date: 2017-10-30 12:38:25 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:06:54 -0400 (Thu, 12 Apr 2018).
| Package 612/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| graph 1.56.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: graph |
| Version: 1.56.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.56.0.tar.gz |
| StartedAt: 2018-04-12 00:05:09 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:06:16 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 67.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/graph.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.56.0’
* 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.
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 compiled code ... OK
* checking installed files from ‘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
‘/home/biocbuild/bbs-3.6-bioc/meat/graph.Rcheck/00check.log’
for details.
graph.Rcheck/00install.out
* installing *source* package ‘graph’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR mv graph.so BioC_graph.so installing to /home/biocbuild/bbs-3.6-bioc/meat/graph.Rcheck/graph/libs ** R ** data ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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 -- Thu Apr 12 00:06:11 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
Warning message:
In readLines(con) : seek on a gzfile connection returned an internal error
>
> proc.time()
user system elapsed
18.836 0.092 18.943
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.048 | 0.004 | 0.054 | |
| IMCA | 0.112 | 0.004 | 0.117 | |
| MAPKsig | 0.412 | 0.008 | 0.427 | |
| MultiGraph-class | 0.480 | 0.000 | 0.481 | |
| acc-methods | 0.080 | 0.000 | 0.079 | |
| addEdge | 0.036 | 0.000 | 0.035 | |
| addNode | 0.020 | 0.000 | 0.018 | |
| adj-methods | 0.004 | 0.000 | 0.004 | |
| adjacencyMatrix | 0.004 | 0.000 | 0.003 | |
| apoptosisGraph | 0.012 | 0.000 | 0.013 | |
| attrData-class | 0.004 | 0.000 | 0.002 | |
| aveNumEdges | 0.004 | 0.000 | 0.003 | |
| biocRepos | 0.000 | 0.000 | 0.002 | |
| boundary | 0.000 | 0.000 | 0.004 | |
| calcProb | 0.000 | 0.000 | 0.001 | |
| calcSumProb | 0.052 | 0.004 | 0.058 | |
| clearNode | 0.016 | 0.000 | 0.013 | |
| clusterGraph-class | 0.008 | 0.000 | 0.007 | |
| clusteringCoefficient-methods | 0.024 | 0.000 | 0.025 | |
| combineNodes | 0.092 | 0.000 | 0.096 | |
| distGraph-class | 0.000 | 0.000 | 0.002 | |
| duplicatedEdges | 0.000 | 0.000 | 0.001 | |
| edgeMatrix | 0.028 | 0.004 | 0.033 | |
| edgeSets | 0.032 | 0.000 | 0.033 | |
| edgeWeights | 0.008 | 0.000 | 0.007 | |
| fromGXL-methods | 0.448 | 0.000 | 0.448 | |
| graph-class | 0.008 | 0.000 | 0.008 | |
| graph2SparseM | 0.092 | 0.008 | 0.102 | |
| graphAM-class | 0.028 | 0.000 | 0.029 | |
| graphBAM-class | 0.208 | 0.000 | 0.210 | |
| graphExamples | 0.004 | 0.000 | 0.003 | |
| graphNEL-class | 0.004 | 0.000 | 0.007 | |
| inEdges | 0.004 | 0.000 | 0.005 | |
| leaves | 0.004 | 0.004 | 0.008 | |
| listEdges | 0.012 | 0.000 | 0.010 | |
| matrix2Graph | 0.028 | 0.000 | 0.026 | |
| mostEdges | 0.004 | 0.000 | 0.006 | |
| numNoEdges | 0.000 | 0.000 | 0.002 | |
| pancrCaIni | 0.172 | 0.000 | 0.169 | |
| randomEGraph | 0.004 | 0.000 | 0.004 | |
| randomGraph | 0.000 | 0.000 | 0.003 | |
| randomNodeGraph | 0.004 | 0.000 | 0.003 | |
| removeEdge | 0.036 | 0.000 | 0.036 | |
| removeNode | 0.004 | 0.000 | 0.006 | |
| renderInfo-class | 0.048 | 0.004 | 0.052 | |
| reverseEdgeDirections | 0.000 | 0.000 | 0.004 | |
| simpleEdge-class | 0.000 | 0.000 | 0.001 | |
| standardLabeling | 0.064 | 0.000 | 0.063 | |
| subGraph | 0.000 | 0.000 | 0.001 | |
| toDotR-methods | 0.032 | 0.000 | 0.035 | |
| ugraph | 0.012 | 0.000 | 0.010 | |
| validGraph | 0.000 | 0.000 | 0.001 | |