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BioC 3.2: CHECK report for gage on perceval

This page was generated on 2015-05-25 10:02:36 -0700 (Mon, 25 May 2015).

Package 364/1029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.19.0
Weijun Luo
Snapshot Date: 2015-05-24 16:31:12 -0700 (Sun, 24 May 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gage
Last Changed Rev: 102594 / Revision: 104161
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gage
Version: 2.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gage_2.19.0.tar.gz
StartedAt: 2015-05-25 00:55:57 -0700 (Mon, 25 May 2015)
EndedAt: 2015-05-25 00:58:20 -0700 (Mon, 25 May 2015)
EllapsedTime: 143.0 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_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gage.Rcheck’
* using R version 3.2.0 Patched (2015-04-19 r68206)
* 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 ‘2.19.0’
* 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 ... [11s/11s] 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 ... [26s/29s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/gage.Rcheck/00check.log’
for details.

gage.Rcheck/00install.out:

* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gage)

gage.Rcheck/gage-Ex.timings:

nameusersystemelapsed
eg2sym2.0600.1712.232
egSymb1.4260.1441.571
essGene0.6590.0280.688
esset.grp1.8580.1021.962
gage3.3840.1893.573
gageComp1.7720.1421.985
gagePipe1.2710.1181.392
geneData0.6970.0420.739
go.gsets0.0030.0010.004
gs.tTest0.3510.0350.387
gse168730.3610.0270.388
heter.gage0.7900.0620.852
kegg.gs1.9080.1762.086
kegg.gsets1.1290.0614.934
readExpData0.0120.0000.012
readList0.2310.0190.251
sigGeneSet0.8310.0500.883