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BioC 3.2: CHECK report for graph on zin1

This page was generated on 2015-08-24 10:46:38 -0700 (Mon, 24 Aug 2015).

Package 449/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.47.2
Bioconductor Package Maintainer
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph
Last Changed Rev: 104759 / Revision: 107696
Last Changed Date: 2015-06-09 14:26:38 -0700 (Tue, 09 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: graph
Version: 1.47.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.47.2.tar.gz
StartedAt: 2015-08-24 00:34:20 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:35:17 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 57.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: graph.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.47.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/graph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.47.2’
* 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 ... [4s/4s] 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
gxlTreeNEL: no visible global function definition for ‘xmlOutputDOM’
combineNodes,character-graphNEL-character : .local: no visible binding
  for global variable ‘from’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘dist’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [14s/14s]
 [14s/14s] 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-3.2-bioc/meat/graph.Rcheck/00check.log’
for details.


graph.Rcheck/00install.out:

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.2-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
DFS0.0240.0000.025
IMCA0.1490.0000.149
MAPKsig0.1380.0080.147
MultiGraph-class0.0660.0040.070
acc-methods0.0110.0000.011
addEdge0.0080.0000.007
addNode0.0090.0000.009
adj-methods0.0030.0000.004
adjacencyMatrix0.0030.0000.003
apoptosisGraph0.0240.0000.024
attrData-class0.0020.0000.002
aveNumEdges0.0080.0000.009
biocRepos0.0020.0000.002
boundary0.0050.0000.006
calcProb0.0010.0000.000
calcSumProb0.0050.0000.006
clearNode0.0080.0000.009
clusterGraph-class0.0030.0000.004
clusteringCoefficient-methods0.0070.0000.008
combineNodes0.0250.0000.038
distGraph-class0.0010.0000.001
duplicatedEdges0.0010.0000.001
edgeMatrix0.0090.0030.012
edgeSets0.0350.0040.039
edgeWeights0.0060.0000.006
fromGXL-methods0.2690.0160.285
graph-class0.0070.0000.007
graph2SparseM0.0980.0000.099
graphAM-class0.0090.0000.009
graphBAM-class0.0330.0040.037
graphExamples0.0040.0000.004
graphNEL-class0.0000.0040.004
inEdges0.0010.0000.003
leaves0.010.000.01
listEdges0.0090.0000.009
matrix2Graph0.0220.0000.022
mostEdges0.0170.0000.017
numNoEdges0.0040.0000.004
pancrCaIni0.0870.0040.091
randomEGraph0.0060.0000.006
randomGraph0.0070.0000.007
randomNodeGraph0.0040.0000.004
removeEdge0.0060.0000.006
removeNode0.0000.0000.003
renderInfo-class0.0080.0000.008
reverseEdgeDirections0.0060.0000.005
simpleEdge-class0.0010.0000.002
standardLabeling0.070.000.07
subGraph0.0020.0000.002
toDotR-methods0.0240.0040.024
ugraph0.0040.0000.006
validGraph0.0010.0000.002