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BioC 3.1: CHECK report for gage on petty

This page was generated on 2015-10-09 09:34:16 -0700 (Fri, 09 Oct 2015).

Package 361/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.18.0
Weijun Luo
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gage
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gage
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gage_2.18.0.tar.gz
StartedAt: 2015-10-08 23:05:57 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:09:00 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 182.7 seconds
RetCode: 0
Status:  OK 
CheckDir: gage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gage_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gage.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gage’ can be installed ... [15s/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 ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
deComp: no visible global function definition for ‘annot.db’
eg2sym: no visible binding for global variable ‘egSymb’
esset.grp: no visible global function definition for ‘nodes’
esset.grp: no visible global function definition for ‘edgeNames’
esset.grp: no visible global function definition for ‘make.graph’
esset.grp : <anonymous>: no visible global function definition for
  ‘nodes’
go.gsets: no visible global function definition for ‘biocLite’
go.gsets: no visible binding for global variable ‘GOTERM’
kegg.gsets: no visible binding for global variable ‘khier’
kegg.species.code: no visible binding for global variable ‘korg’
sym2eg: no visible binding for global variable ‘egSymb’
* 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 ... [31s/36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
kegg.gsets 1.174  0.059   5.723
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/gage.Rcheck/00check.log’
for details.


gage.Rcheck/00install.out:

* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (gage)

gage.Rcheck/gage-Ex.timings:

nameusersystemelapsed
eg2sym1.9360.1182.054
egSymb1.9060.1302.037
essGene0.6080.0320.653
esset.grp2.9720.1083.083
gage4.5620.1824.749
gageComp1.9810.1372.225
gagePipe1.9570.1182.085
geneData0.4230.0330.469
go.gsets0.0050.0010.006
gs.tTest0.4180.0250.443
gse168730.4720.0250.498
heter.gage1.4470.0691.519
kegg.gs2.0710.1502.221
kegg.gsets1.1740.0595.723
readExpData0.0150.0010.016
readList0.3150.0170.334
sigGeneSet1.0150.0541.076