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: 2017-10-18 05:17:01 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:20:16 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 195.5 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 3.4.2 (2017-09-28)
* 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            15.815  1.408  17.861
add_edge_data           13.849  0.929  15.304
add_KEGG_drugs           9.210  0.292  14.948
path_genes_by_cell_type  7.440  0.507   8.730
edge_mapping_info        7.084  0.517   7.962
refine_mappings          6.806  0.456   7.628
get_graph_object         5.885  0.231   6.462
* 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	9.210	0.292	14.948
add_edge_data	13.849	0.929	15.304
cyto_vis	0.530	0.079	0.836
edge_mapping_info	7.084	0.517	7.962
expand_KEGG_edges	0.272	0.003	0.518
expand_KEGG_mappings	0.146	0.001	0.369
generate_mappings	0.001	0.000	0.001
get_KGML	0.146	0.001	0.868
get_drug_table	0.167	0.001	0.975
get_fisher_info	0.003	0.000	0.003
get_graph_object	5.885	0.231	6.462
node_mapping_info	0.159	0.001	0.406
overlap_info	15.815	1.408	17.861
path_genes_by_cell_type	7.440	0.507	8.730
refine_mappings	6.806	0.456	7.628