BioC 3.6: CHECK report for CEMiTool on tokay1

Package: CEMiTool

Version: 0.99.8

Command: rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_0.99.8.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_0.99.8.tar.gz

StartedAt: 2017-08-15 22:16:11 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:23:13 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 422.3 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_0.99.8.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_0.99.8.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       1.2Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plot_interactions 11.32   0.13   11.44
generate_report    3.39   0.34   25.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plot_interactions 11.08   0.17   11.25
find_modules       6.10   0.02    6.12
generate_report    5.14   0.36   19.03
plot_ora           5.30   0.00    5.29
plot_gsea          5.15   0.00    5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_0.99.8.zip
* DONE (CEMiTool)

name	user	system	elapsed
CEMiTool-class	0.02	0.00	0.02
cem	0.03	0.00	0.04
cemitool	0	0	0
cemoverlap	0	0	0
expr	0.00	0.01	0.01
expr_data	0.03	0.00	0.03
filter_expr	0.34	0.03	0.38
find_modules	3.69	0.05	3.73
generate_report	3.39	0.34	25.99
get_hubs	0.03	0.00	0.03
gsea_data	3.36	0.02	3.37
interactions_data	0.67	0.05	0.74
mod_colors	0.02	0.01	0.03
mod_gsea	3.20	0.02	3.22
mod_ora	3.34	0.06	3.41
mod_summary	0.05	0.00	1.95
module_genes	0.03	0.01	0.04
module_names	0.36	0.00	0.36
new_cem	0.02	0.02	0.03
nmodules	0.01	0.00	0.02
ora_data	3.30	0.04	3.34
plot_beta_r2	0.70	0.00	0.71
plot_gsea	4.59	0.00	4.59
plot_interactions	11.32	0.13	11.44
plot_mean_k	0.29	0.00	0.30
plot_ora	4.35	0.09	4.68
plot_profile	1.84	0.03	1.88
read_gmt	0.86	0.00	0.86
sample_annot	0	0	0
sample_annotation	0.03	0.00	0.03
show_plot	0.25	0.00	0.25
write_files	0.03	0.00	0.06

name	user	system	elapsed
CEMiTool-class	0.03	0.00	0.03
cem	0.03	0.02	0.05
cemitool	0	0	0
cemoverlap	0	0	0
expr	0	0	0
expr_data	0.03	0.01	0.05
filter_expr	0.44	0.06	0.50
find_modules	6.10	0.02	6.12
generate_report	5.14	0.36	19.03
get_hubs	0.03	0.02	0.05
gsea_data	3.73	0.00	3.73
interactions_data	0.69	0.03	0.72
mod_colors	0.05	0.00	0.05
mod_gsea	2.48	0.00	2.48
mod_ora	3.93	0.01	3.95
mod_summary	0.05	0.00	0.05
module_genes	0.03	0.00	0.03
module_names	0.03	0.00	0.03
new_cem	0.02	0.00	0.02
nmodules	0.06	0.00	0.06
ora_data	3.84	0.03	3.87
plot_beta_r2	0.93	0.02	0.94
plot_gsea	5.15	0.00	5.16
plot_interactions	11.08	0.17	11.25
plot_mean_k	0.34	0.00	0.35
plot_ora	5.30	0.00	5.29
plot_profile	3.20	0.00	3.21
read_gmt	1.52	0.00	1.51
sample_annot	0	0	0
sample_annotation	0.01	0.02	0.03
show_plot	0.27	0.00	0.27
write_files	0.01	0.01	0.03