BioC 3.5: CHECK report for EWCE on oaxaca

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: 2017-03-04 02:33:43 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:35:58 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 135.2 seconds

RetCode: 0

Status:  OK

CheckDir: EWCE.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EWCE_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EWCE.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 5.662  0.149  43.106
* 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.

* 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)

name	user	system	elapsed
add.res.to.merging.list	1.701	0.057	1.758
bootstrap.enrichment.test	5.662	0.149	43.106
ewce.plot	1.425	0.025	1.449
ewce_expression_data	0.247	0.010	0.257
generate.bootstrap.plots	4.182	0.050	4.238
merged_ewce	0.441	0.004	0.445
mouse_to_human_homologs	0.001	0.000	0.001
read_celltype_data	0.000	0.001	0.000