BioC 3.6: CHECK report for KEGGlincs on malbec1

Package: KEGGlincs

Version: 1.3.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings KEGGlincs_1.3.2.tar.gz

StartedAt: 2017-08-16 00:16:25 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:19:37 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 191.5 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.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 KEGGlincs_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/KEGGlincs.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 ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.3.2’
* 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            15.412  1.608  17.301
add_edge_data           15.452  1.076  17.688
add_KEGG_drugs          10.616  0.068  16.712
edge_mapping_info        8.552  0.776   9.610
path_genes_by_cell_type  7.960  0.796   9.033
refine_mappings          6.368  0.428   7.164
get_graph_object         6.048  0.028   6.345
* 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	0.000	0.000	0.001
add_KEGG_drugs	10.616	0.068	16.712
add_edge_data	15.452	1.076	17.688
cyto_vis	0.492	0.000	0.771
edge_mapping_info	8.552	0.776	9.610
expand_KEGG_edges	0.336	0.000	0.590
expand_KEGG_mappings	0.192	0.000	0.461
generate_mappings	0.000	0.000	0.001
get_KGML	0.176	0.000	0.962
get_drug_table	0.216	0.000	1.327
get_fisher_info	0.004	0.000	0.003
get_graph_object	6.048	0.028	6.345
node_mapping_info	0.284	0.004	0.585
overlap_info	15.412	1.608	17.301
path_genes_by_cell_type	7.960	0.796	9.033
refine_mappings	6.368	0.428	7.164
tidy_edge	0	0	0