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BioC 3.2: CHECK report for graph on moscato1

This page was generated on 2015-08-20 13:17:38 -0700 (Thu, 20 Aug 2015).

Package 448/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.47.2
Bioconductor Package Maintainer
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph
Last Changed Rev: 104759 / Revision: 107602
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
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 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: rm -rf graph.buildbin-libdir graph.Rcheck && mkdir graph.buildbin-libdir graph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graph.buildbin-libdir graph_1.47.2.tar.gz >graph.Rcheck\00install.out 2>&1 && cp graph.Rcheck\00install.out graph-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=graph.buildbin-libdir --install="check:graph-install.out" --force-multiarch --no-vignettes --timings graph_1.47.2.tar.gz
StartedAt: 2015-08-20 05:31:33 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 05:34:23 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 169.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: graph.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf graph.buildbin-libdir graph.Rcheck && mkdir graph.buildbin-libdir graph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graph.buildbin-libdir graph_1.47.2.tar.gz >graph.Rcheck\00install.out 2>&1 && cp graph.Rcheck\00install.out graph-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=graph.buildbin-libdir --install="check:graph-install.out" --force-multiarch --no-vignettes --timings graph_1.47.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/graph.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/graph.buildbin-libdir/graph/libs/i386/BioC_graph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/graph.buildbin-libdir/graph/libs/x64/BioC_graph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'graph_unit_tests.R' [17s]
 [17s] OK
** running tests for arch 'x64' ...
  Running 'graph_unit_tests.R' [21s]
 [21s] 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, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/graph.Rcheck/00check.log'
for details.


graph.Rcheck/00install.out:


install for i386

* installing *source* package 'graph' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
gcc -m32 -shared -s -static-libgcc -o graph.dll tmp.def graph.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
mv graph.dll BioC_graph.dll
installing to D:/biocbld/bbs-3.2-bioc/meat/graph.buildbin-libdir/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'graph' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
gcc -m64 -shared -s -static-libgcc -o graph.dll tmp.def graph.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
mv graph.dll BioC_graph.dll
installing to D:/biocbld/bbs-3.2-bioc/meat/graph.buildbin-libdir/graph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graph' as graph_1.47.2.zip
* DONE (graph)

graph.Rcheck/examples_i386/graph-Ex.timings:

nameusersystemelapsed
DFS0.010.000.02
IMCA0.190.000.18
MAPKsig0.110.000.11
MultiGraph-class0.070.000.08
acc-methods0.020.000.02
addEdge000
addNode0.020.000.01
adj-methods000
adjacencyMatrix000
apoptosisGraph0.020.000.01
attrData-class000
aveNumEdges000
biocRepos0.020.000.01
boundary000
calcProb000
calcSumProb0.010.000.02
clearNode000
clusterGraph-class000
clusteringCoefficient-methods000
combineNodes0.030.000.03
distGraph-class000
duplicatedEdges000
edgeMatrix0.020.000.01
edgeSets0.040.000.05
edgeWeights000
fromGXL-methods0.340.001.02
graph-class0.020.000.01
graph2SparseM0.140.000.14
graphAM-class0.010.000.02
graphBAM-class0.070.000.06
graphExamples000
graphNEL-class000
inEdges000
leaves0.030.000.03
listEdges0.010.000.01
matrix2Graph0.020.000.02
mostEdges0.010.000.02
numNoEdges0.020.000.01
pancrCaIni0.090.000.10
randomEGraph000
randomGraph000
randomNodeGraph000
removeEdge0.010.000.02
removeNode000
renderInfo-class0.020.000.01
reverseEdgeDirections0.020.000.02
simpleEdge-class000
standardLabeling0.150.000.15
subGraph0.020.000.02
toDotR-methods0.030.000.03
ugraph000
validGraph000

graph.Rcheck/examples_x64/graph-Ex.timings:

nameusersystemelapsed
DFS0.030.000.03
IMCA0.250.000.25
MAPKsig0.240.000.30
MultiGraph-class0.090.000.09
acc-methods0.020.000.02
addEdge0.020.000.02
addNode0.010.000.01
adj-methods000
adjacencyMatrix000
apoptosisGraph0.030.000.03
attrData-class0.020.000.02
aveNumEdges000
biocRepos0.000.020.01
boundary000
calcProb000
calcSumProb0.010.000.02
clearNode000
clusterGraph-class000
clusteringCoefficient-methods000
combineNodes0.050.000.05
distGraph-class000
duplicatedEdges000
edgeMatrix0.010.000.02
edgeSets0.050.000.04
edgeWeights0.010.000.02
fromGXL-methods0.360.010.41
graph-class0.020.000.01
graph2SparseM0.150.000.16
graphAM-class0.020.000.01
graphBAM-class0.060.000.06
graphExamples0.020.000.02
graphNEL-class000
inEdges000
leaves0.010.000.02
listEdges0.020.000.01
matrix2Graph0.050.000.05
mostEdges0.010.000.01
numNoEdges0.020.000.02
pancrCaIni0.120.000.12
randomEGraph000
randomGraph0.020.000.02
randomNodeGraph000
removeEdge0.010.000.02
removeNode000
renderInfo-class0.020.000.01
reverseEdgeDirections000
simpleEdge-class0.010.000.02
standardLabeling0.080.000.07
subGraph000
toDotR-methods0.030.000.03
ugraph0.020.000.02
validGraph000