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BioC 3.5: CHECK report for EGSEA on malbec2

This page was generated on 2017-08-16 13:17:36 -0400 (Wed, 16 Aug 2017).

Package 392/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGSEA 1.4.1
Monther Alhamdoosh
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/EGSEA
Last Changed Rev: 131409 / Revision: 131943
Last Changed Date: 2017-07-19 23:15:42 -0400 (Wed, 19 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EGSEA
Version: 1.4.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings EGSEA_1.4.1.tar.gz
StartedAt: 2017-08-15 22:45:42 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:52:36 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 414.2 seconds
RetCode: 0
Status:  OK 
CheckDir: EGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings EGSEA_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/EGSEA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EGSEA/DESCRIPTION’ ... OK
* this is package ‘EGSEA’ version ‘1.4.1’
* 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 ‘EGSEA’ 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’
buildMSigDBIdx: no visible binding for global variable ‘msigdb’
generateSummaryPlots: no visible binding for global variable ‘x.data’
generateSummaryPlots: no visible binding for global variable ‘y.data’
generateSummaryPlots: no visible binding for global variable ‘gsSize’
generateSummaryPlots: no visible binding for global variable ‘id’
generateSummaryPlots: no visible binding for global variable ‘sig’
loadKeggData: no visible binding for global variable ‘kegg.pathways’
plotBars,EGSEAResults: no visible global function definition for
  ‘abline’
Undefined global functions or variables:
  GOTERM abline gsSize id kegg.pathways msigdb sig x.data y.data
Consider adding
  importFrom("graphics", "abline")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
EGSEAResults-methods 77.240  0.552  82.342
buildGeneSetDBIdx    30.672  0.096  30.804
egsea.cnt            26.216  2.276  17.225
egsea                14.424  1.188  16.301
buildIdx              9.256  0.032   9.331
buildMSigDBIdx        5.960  0.016   5.984
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/EGSEA.Rcheck/00check.log’
for details.


EGSEA.Rcheck/00install.out:

* installing *source* package ‘EGSEA’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (EGSEA)

EGSEA.Rcheck/EGSEA-Ex.timings:

nameusersystemelapsed
EGSEAResults-methods77.240 0.55282.342
GSCollectionIndex-methods3.1040.0723.199
buildCustomIdx0.3720.0400.414
buildGeneSetDBIdx30.672 0.09630.804
buildIdx9.2560.0329.331
buildKEGGIdx0.5160.0040.521
buildMSigDBIdx5.9600.0165.984
egsea14.424 1.18816.301
egsea.base0.0040.0000.000
egsea.cnt26.216 2.27617.225
egsea.combine0.0000.0000.001
egsea.ora2.4800.1082.603
egsea.sort000