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BioC 2.13: CHECK report for DEGraph on moscato1

This page was generated on 2014-04-05 09:50:12 -0700 (Sat, 05 Apr 2014).

Package 196/750HostnameOS / ArchBUILDCHECKBUILD BIN
DEGraph 1.14.0
Laurent Jacob
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/DEGraph
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: DEGraph
Version: 1.14.0
Command: rm -rf DEGraph.buildbin-libdir && mkdir DEGraph.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.14.0.tar.gz >DEGraph-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.14.0.tar.gz && mv DEGraph.buildbin-libdir/* DEGraph.Rcheck/ && rmdir DEGraph.buildbin-libdir
StartedAt: 2014-04-05 03:25:37 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:29:41 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 243.6 seconds
RetCode: 0
Status:  OK  
CheckDir: DEGraph.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/DEGraph.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.14.0'
* 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 whether package 'DEGraph' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph' 'KEGGgraph' 'lattice' 'RBGL' 'rrcov' 'Rgraphviz' 'NCIgraph'
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'R.utils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'graph:::getIndices'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'DEGraph.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [62s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getKEGGPathways 9.31   0.00   14.15
testOneGraph    8.12   0.01    8.13
plotValuedGraph 7.43   0.05    8.14
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotValuedGraph 10.08   0.06   10.14
getKEGGPathways  9.41   0.06    9.68
testOneGraph     8.89   0.04    8.94
hyper.test       6.58   0.06    6.65
BS.test          5.41   0.06    5.48
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/DEGraph.Rcheck/00check.log'
for details.

DEGraph.Rcheck/00install.out:


install for i386

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'DEGraph' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'DEGraph' as DEGraph_1.14.0.zip
* DONE (DEGraph)

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

nameusersystemelapsed
AN.test4.000.034.02
BS.test3.650.033.70
annLoi20080.340.000.35
classLoi20080.240.010.24
exprLoi20080.250.000.25
getConnectedComponentList2.450.002.45
getKEGGPathways 9.31 0.0014.15
getSignedGraph3.080.003.07
grListKEGG1.310.001.31
graph.T2.test1.940.021.95
hyper.test4.300.014.32
laplacianFromA0.440.050.81
plotValuedGraph7.430.058.14
randomWAMGraph0.380.030.61
testOneConnectedComponent2.390.022.41
testOneGraph8.120.018.13
twoSampleFromGraph0.560.030.79
writeAdjacencyMatrix2KGML0.420.030.66

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

nameusersystemelapsed
AN.test4.130.074.20
BS.test5.410.065.48
annLoi20080.390.000.39
classLoi20080.260.000.27
exprLoi20080.220.000.21
getConnectedComponentList2.540.002.55
getKEGGPathways9.410.069.68
getSignedGraph2.450.002.44
grListKEGG1.430.021.45
graph.T2.test2.910.002.91
hyper.test6.580.066.65
laplacianFromA0.580.000.80
plotValuedGraph10.08 0.0610.14
randomWAMGraph0.390.020.61
testOneConnectedComponent2.470.002.46
testOneGraph8.890.048.94
twoSampleFromGraph0.510.040.74
writeAdjacencyMatrix2KGML0.560.010.78