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BioC 3.0: CHECK report for graph on perceval

This page was generated on 2015-04-10 09:51:53 -0700 (Fri, 10 Apr 2015).

Package 399/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.44.1
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/graph
Last Changed Rev: 97479 / Revision: 102249
Last Changed Date: 2014-12-08 12:32:09 -0800 (Mon, 08 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: graph
Version: 1.44.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.44.1.tar.gz
StartedAt: 2015-04-10 02:28:03 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:29:58 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 114.9 seconds
RetCode: 0
Status:  OK 
CheckDir: graph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.44.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/graph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.44.1’
* 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 ... [7s/15s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [25s/25s]
 [25s/26s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/graph.Rcheck/00check.log’
for details.

graph.Rcheck/00install.out:

* installing *source* package ‘graph’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c graph.c -o graph.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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 /Users/biocbuild/bbs-3.0-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
DFS0.0450.0010.046
IMCA0.3390.0130.353
MAPKsig0.2220.0070.227
MultiGraph-class0.1640.0030.167
acc-methods0.0110.0010.012
addEdge0.0080.0000.009
addNode0.0080.0000.009
adj-methods0.0040.0010.004
adjacencyMatrix0.0030.0010.004
apoptosisGraph0.0630.0050.068
attrData-class0.0030.0010.004
aveNumEdges0.0130.0010.014
biocRepos0.0020.0000.003
boundary0.0090.0000.010
calcProb000
calcSumProb0.0080.0000.008
clearNode0.0110.0000.011
clusterGraph-class0.0040.0000.004
clusteringCoefficient-methods0.0090.0000.009
combineNodes0.0350.0000.036
distGraph-class0.0020.0000.002
duplicatedEdges000
edgeMatrix0.0130.0000.014
edgeSets0.0400.0110.052
edgeWeights0.0120.0010.012
fromGXL-methods0.4860.0150.511
graph-class0.0120.0020.014
graph2SparseM0.1860.0080.194
graphAM-class0.0140.0010.014
graphBAM-class0.1910.0020.193
graphExamples0.0060.0010.006
graphNEL-class0.0060.0010.006
inEdges0.0040.0000.003
leaves0.0160.0040.020
listEdges0.0150.0030.018
matrix2Graph0.0260.0020.028
mostEdges0.0220.0020.024
numNoEdges0.0070.0010.007
pancrCaIni0.1300.0040.215
randomEGraph0.0080.0010.008
randomGraph0.0060.0000.006
randomNodeGraph0.0050.0010.005
removeEdge0.0110.0000.012
removeNode0.0030.0000.004
renderInfo-class0.0090.0010.010
reverseEdgeDirections0.0070.0000.006
simpleEdge-class0.0020.0010.002
standardLabeling0.0560.0040.061
subGraph0.0030.0000.003
toDotR-methods0.0290.0040.141
ugraph0.0070.0000.007
validGraph0.0020.0000.002