BioC 3.6: CHECK report for CEMiTool on malbec1

Package: CEMiTool

Version: 0.99.8

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_0.99.8.tar.gz

StartedAt: 2017-08-15 21:49:37 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:53:26 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 228.4 seconds

RetCode: 0

Status: OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_0.99.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CEMiTool.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 ‘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  8.6Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       2.3Mb
    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   7.988  1.044  14.378
plot_interactions 8.456  0.032   8.496
* 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
  ‘/home/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	0.032	0.004	0.037
cem	0.024	0.000	0.024
cemitool	0.000	0.000	0.001
cemoverlap	0.000	0.000	0.001
expr	0.000	0.000	0.001
expr_data	0.036	0.004	0.038
filter_expr	0.692	0.004	0.694
find_modules	3.804	0.004	3.844
generate_report	7.988	1.044	14.378
get_hubs	0.032	0.000	0.030
gsea_data	2.988	0.044	2.965
interactions_data	1.044	0.036	1.079
mod_colors	0.02	0.00	0.02
mod_gsea	2.840	0.004	2.771
mod_ora	3.052	0.004	3.057
mod_summary	0.052	0.000	0.043
module_genes	0.040	0.004	0.040
module_names	0.020	0.000	0.022
new_cem	0.044	0.000	0.047
nmodules	0.020	0.000	0.021
ora_data	3.324	0.008	3.331
plot_beta_r2	0.692	0.000	0.692
plot_gsea	3.680	0.000	3.601
plot_interactions	8.456	0.032	8.496
plot_mean_k	0.268	0.000	0.269
plot_ora	4.012	0.012	4.024
plot_profile	1.852	0.004	1.860
read_gmt	0.884	0.004	0.892
sample_annot	0.000	0.000	0.002
sample_annotation	0.020	0.000	0.017
show_plot	0.212	0.004	0.216
write_files	0.024	0.000	0.024

BioC 3.6: CHECK report for CEMiTool on malbec1

Summary

Command output