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BioC 3.5: CHECK report for graph on malbec2

This page was generated on 2017-08-16 13:12:09 -0400 (Wed, 16 Aug 2017).

Package 588/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.54.0
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/graph
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graph
Version: 1.54.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.54.0.tar.gz
StartedAt: 2017-08-15 23:37:56 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:39:03 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 67.1 seconds
RetCode: 0
Status:  OK 
CheckDir: graph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/graph.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.54.0’
* 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-3.5-bioc/meat/graph.Rcheck/00check.log’
for details.


graph.Rcheck/00install.out:

* installing *source* package ‘graph’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.5-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/graph-Ex.timings:

nameusersystemelapsed
DFS0.0480.0000.049
IMCA0.1400.0040.144
MAPKsig0.2920.0000.292
MultiGraph-class0.4760.0040.481
acc-methods0.0800.0000.081
addEdge0.0400.0000.039
addNode0.020.000.02
adj-methods0.0080.0000.006
adjacencyMatrix0.0040.0000.002
apoptosisGraph0.0120.0000.012
attrData-class0.0000.0000.001
aveNumEdges0.0040.0000.003
biocRepos0.0000.0000.002
boundary0.0000.0040.003
calcProb000
calcSumProb0.0560.0000.057
clearNode0.0120.0000.012
clusterGraph-class0.0080.0000.008
clusteringCoefficient-methods0.0280.0000.026
combineNodes0.0960.0000.096
distGraph-class0.0040.0000.001
duplicatedEdges0.0000.0000.001
edgeMatrix0.0320.0000.034
edgeSets0.0520.0040.057
edgeWeights0.0120.0000.013
fromGXL-methods0.4160.0120.429
graph-class0.0040.0000.008
graph2SparseM0.0920.0040.098
graphAM-class0.0360.0000.033
graphBAM-class0.2320.0000.233
graphExamples0.0080.0000.007
graphNEL-class0.0080.0040.010
inEdges0.0080.0000.010
leaves0.0120.0000.013
listEdges0.0200.0000.017
matrix2Graph0.0400.0000.041
mostEdges0.0080.0000.009
numNoEdges0.0040.0000.004
pancrCaIni0.2520.0000.253
randomEGraph0.0080.0000.006
randomGraph0.0080.0000.005
randomNodeGraph0.0040.0000.004
removeEdge0.0520.0040.056
removeNode0.0080.0000.008
renderInfo-class0.0800.0000.078
reverseEdgeDirections0.0040.0000.006
simpleEdge-class0.0000.0000.001
standardLabeling0.0920.0000.090
subGraph0.0040.0000.003
toDotR-methods0.040.000.04
ugraph0.0080.0000.007
validGraph0.0040.0000.001