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BioC 2.13: CHECK report for clipper on moscato1

This page was generated on 2014-04-05 09:51:11 -0700 (Sat, 05 Apr 2014).

Package 143/750HostnameOS / ArchBUILDCHECKBUILD BIN
clipper 1.2.3
Paolo Martini
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/clipper
Last Changed Rev: 87799 / Revision: 88450
Last Changed Date: 2014-03-24 10:23:01 -0700 (Mon, 24 Mar 2014)
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: clipper
Version: 1.2.3
Command: rm -rf clipper.buildbin-libdir && mkdir clipper.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.2.3.tar.gz >clipper-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.2.3.tar.gz && mv clipper.buildbin-libdir/* clipper.Rcheck/ && rmdir clipper.buildbin-libdir
StartedAt: 2014-04-05 03:04:46 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:11:09 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 383.4 seconds
RetCode: 0
Status:  OK  
CheckDir: clipper.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/clipper.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 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' version '1.2.3'
* 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 'clipper' 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
Namespace in Imports field not imported from: 'KEGGgraph'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Matrix' 'graph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'clipper.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [40s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pathwayTest 12.08   0.04   12.12
clipper      6.77   0.08    6.98
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pathwayTest 10.40   0.04   10.45
clipper      6.85   0.09    7.02
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [15s]
 [15s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [16s]
 [16s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/clipper.Rcheck/00check.log'
for details.

clipper.Rcheck/00install.out:


install for i386

* installing *source* package 'clipper' ...
** R
** 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 'clipper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clipper' as clipper_1.2.3.zip
* DONE (clipper)

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

nameusersystemelapsed
clipper6.770.086.98
cliqueMeanTest3.620.083.70
cliqueVarianceTest3.370.003.37
deleteEdge0.250.000.25
easyClip3.150.023.23
getGraphEntryGenes0.370.000.38
getJunctionTreePaths0.380.000.37
nameCliques0.010.000.02
pathwayTest12.08 0.0412.12
plotInCytoscape000
prunePaths0.010.000.02

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

nameusersystemelapsed
clipper6.850.097.02
cliqueMeanTest3.500.083.57
cliqueVarianceTest3.200.083.28
deleteEdge0.270.000.26
easyClip3.080.053.12
getGraphEntryGenes0.350.000.34
getJunctionTreePaths0.320.000.33
nameCliques0.020.000.01
pathwayTest10.40 0.0410.45
plotInCytoscape000
prunePaths0.010.000.01