BioC 3.6: CHECK report for CEMiTool on veracruz1

Package: CEMiTool

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CEMiTool_0.99.8.tar.gz

StartedAt: 2017-08-16 00:53:20 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:57:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 252.0 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.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 CEMiTool_0.99.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘0.99.8’
* package encoding: UTF-8
* 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 ‘CEMiTool’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       2.7Mb
    extdata   2.8Mb
* 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
plot_interaction: no visible binding for global variable ‘cem’
read_gmt: no visible binding for global variable ‘stack’
filter_expr,CEMiTool: no visible global function definition for ‘var’
find_modules,CEMiTool: no visible global function definition for ‘tail’
find_modules,CEMiTool: no visible global function definition for ‘head’
find_modules,CEMiTool: no visible global function definition for
  ‘hclust’
find_modules,CEMiTool: no visible global function definition for
  ‘as.dist’
get_hubs,CEMiTool : <anonymous>: no visible global function definition
  for ‘head’
plot_gsea,CEMiTool: no visible global function definition for ‘hclust’
plot_gsea,CEMiTool: no visible global function definition for ‘dist’
plot_ora,CEMiTool : <anonymous>: no visible global function definition
  for ‘head’
Undefined global functions or variables:
  as.dist cem dist hclust head stack tail var
Consider adding
  importFrom("stats", "as.dist", "dist", "hclust", "var")
  importFrom("utils", "head", "stack", "tail")
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
generate_report   11.255  1.268  14.855
plot_interactions 10.726  0.155  11.277
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CEMiTool-class	0.016	0.004	0.021
cem	0.029	0.003	0.037
cemitool	0.001	0.000	0.001
cemoverlap	0.001	0.000	0.000
expr	0.001	0.001	0.002
expr_data	0.032	0.002	0.041
filter_expr	0.424	0.023	0.465
find_modules	4.123	0.047	4.273
generate_report	11.255	1.268	14.855
get_hubs	0.015	0.001	0.020
gsea_data	3.733	0.142	3.611
interactions_data	1.071	0.060	1.028
mod_colors	0.023	0.001	0.025
mod_gsea	3.460	0.128	3.327
mod_ora	3.388	0.130	3.463
mod_summary	0.041	0.007	0.033
module_genes	0.074	0.022	0.033
module_names	0.077	0.017	0.033
new_cem	0.041	0.009	0.017
nmodules	0.045	0.013	0.020
ora_data	3.783	0.110	3.837
plot_beta_r2	0.848	0.004	0.870
plot_gsea	4.098	0.175	3.807
plot_interactions	10.726	0.155	11.277
plot_mean_k	0.340	0.004	0.350
plot_ora	4.388	0.100	4.657
plot_profile	2.260	0.020	2.369
read_gmt	1.102	0.012	1.157
sample_annot	0.002	0.001	0.004
sample_annotation	0.015	0.001	0.016
show_plot	0.297	0.003	0.310
write_files	0.020	0.003	0.024