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BioC 3.5: CHECK report for EWCE on veracruz2

This page was generated on 2017-03-31 14:23:01 -0400 (Fri, 31 Mar 2017).

Package 407/1356HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EWCE 1.3.0
Nathan Skene
Snapshot Date: 2017-03-30 17:16:21 -0400 (Thu, 30 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EWCE
Last Changed Rev: 122712 / Revision: 127890
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  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 

Summary

Package: EWCE
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EWCE_1.3.0.tar.gz
StartedAt: 2017-03-31 02:14:31 -0400 (Fri, 31 Mar 2017)
EndedAt: 2017-03-31 02:21:07 -0400 (Fri, 31 Mar 2017)
EllapsedTime: 395.4 seconds
RetCode: 0
Status:  OK 
CheckDir: EWCE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EWCE_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EWCE.Rcheck’
* using R Under development (unstable) (2017-03-21 r72380)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.3.0’
* 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 ‘EWCE’ 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 loading without being on the library search path ... 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
bootstrap.enrichment.test: no visible global function definition for
  ‘sd’
ewce.plot: no visible global function definition for ‘p.adjust’
ewce_expression_data: no visible global function definition for ‘data’
generate.bootstrap.plots: no visible global function definition for
  ‘pdf’
generate.bootstrap.plots: no visible global function definition for
  ‘dev.off’
merged_ewce: no visible global function definition for ‘sd’
prepare.genesize.control.network: no visible global function definition
  for ‘aggregate’
prepare.genesize.control.network: no visible global function definition
  for ‘data’
prepare.genesize.control.network: no visible global function definition
  for ‘quantile’
read_celltype_data: no visible global function definition for
  ‘read.csv’
read_celltype_data: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate data dev.off p.adjust pdf quantile read.csv sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "aggregate", "p.adjust", "quantile", "sd")
  importFrom("utils", "data", "read.csv")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
bootstrap.enrichment.test 5.002  0.151 306.387
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/EWCE.Rcheck/00check.log’
for details.


EWCE.Rcheck/00install.out:

* installing *source* package ‘EWCE’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EWCE)

EWCE.Rcheck/EWCE-Ex.timings:

nameusersystemelapsed
add.res.to.merging.list1.5240.0551.626
bootstrap.enrichment.test 5.002 0.151306.387
ewce.plot1.2030.0191.244
ewce_expression_data0.4880.0190.524
generate.bootstrap.plots3.5080.0273.598
merged_ewce0.3590.0070.370
mouse_to_human_homologs0.0010.0010.001
read_celltype_data000