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BioC 2.14: CHECK report for PCpheno on petty

This page was generated on 2014-10-08 08:58:12 -0700 (Wed, 08 Oct 2014).

Package 574/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCpheno 1.26.0
Nolwenn Le Meur
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PCpheno
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: PCpheno
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PCpheno_1.26.0.tar.gz
StartedAt: 2014-10-07 23:23:53 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:31:53 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 479.6 seconds
RetCode: 0
Status:  OK 
CheckDir: PCpheno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PCpheno_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PCpheno.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCpheno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCpheno’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Category’ ‘ScISI’ ‘SLGI’ ‘ppiStats’ ‘ppiData’ ‘annotate’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PCpheno’ can be installed ... [40s/43s] 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:
  ‘Category’ ‘ScISI’ ‘KEGG.db’ ‘GO.db’
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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘annotate’ ‘ppiData’ ‘ppiStats’ ‘SLGI’
  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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/76s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
gtResult-class 13.851  1.175  15.113
graphTheory    14.285  0.294  14.658
ppiInteraction  8.928  0.707   9.796
* 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/PCpheno.Rcheck/00check.log’
for details.

PCpheno.Rcheck/00install.out:

* installing *source* package ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (PCpheno)

PCpheno.Rcheck/PCpheno-Ex.timings:

nameusersystemelapsed
CoHyperGResult-class1.1790.0441.287
Dudley0.0120.0110.024
Giaever0.6430.0270.673
HI0.0030.0010.004
KEGG2SCISI0.9840.0361.092
Kastenmayer0.0280.0010.030
Lesage0.0120.0010.013
Osterberg0.0390.0110.050
SGDphenoL0.0460.0090.056
YEASTOHNOLOG0.0140.0010.016
buildFDMat0.7420.0410.784
categoryToEntrezBuilder0.6510.0170.685
complexStatus2.6690.0592.760
deResult-class0.1590.0280.189
densityEstimate3.5040.1163.658
getDescr1.4990.0241.569
getFDgene0.2330.0160.249
graphTheory14.285 0.29414.658
gtResult-class13.851 1.17515.113
overlap0.0040.0000.004
plot2.9160.1873.126
ppiInteraction8.9280.7079.796
reduceM0.0020.0000.003
truncName0.0010.0010.001