BioC 3.5: CHECK report for KEGGlincs on veracruz2

Package: KEGGlincs

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGlincs_1.2.0.tar.gz

StartedAt: 2017-08-16 04:32:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:36:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 207.8 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.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 KEGGlincs_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/KEGGlincs.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 ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.2.0’
* 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 ‘KEGGlincs’ 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
overlap_info            16.397  1.550  18.643
add_edge_data           16.345  1.002  17.965
add_KEGG_drugs          11.117  0.255  17.002
edge_mapping_info        8.268  0.602  10.202
path_genes_by_cell_type  8.087  0.578   9.180
refine_mappings          7.762  0.371   8.618
get_graph_object         6.070  0.210   6.658
* 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: OK

* installing *source* package ‘KEGGlincs’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGlincs)

name	user	system	elapsed
KEGG_lincs	0.001	0.000	0.001
add_KEGG_drugs	11.117	0.255	17.002
add_edge_data	16.345	1.002	17.965
cyto_vis	0.317	0.001	0.578
edge_mapping_info	8.268	0.602	10.202
expand_KEGG_edges	0.303	0.026	0.571
expand_KEGG_mappings	0.219	0.001	0.664
generate_mappings	0.001	0.000	0.001
get_KGML	0.186	0.002	0.943
get_drug_table	0.212	0.001	1.040
get_fisher_info	0.004	0.000	0.004
get_graph_object	6.070	0.210	6.658
node_mapping_info	0.184	0.002	0.435
overlap_info	16.397	1.550	18.643
path_genes_by_cell_type	8.087	0.578	9.180
refine_mappings	7.762	0.371	8.618