BioC 3.5: CHECK report for KEGGlincs on malbec2

Package: KEGGlincs

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings KEGGlincs_1.2.0.tar.gz

StartedAt: 2017-10-18 00:19:22 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:22:28 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 186.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings KEGGlincs_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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
add_edge_data           15.900  0.480  17.181
overlap_info            15.436  0.376  16.074
add_KEGG_drugs          11.484  0.076  17.378
edge_mapping_info        8.100  0.348   8.674
path_genes_by_cell_type  6.444  0.036   6.705
refine_mappings          6.124  0.028   6.452
get_graph_object         6.092  0.024   6.374
* 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	11.484	0.076	17.378
add_edge_data	15.900	0.480	17.181
cyto_vis	0.364	0.000	0.693
edge_mapping_info	8.100	0.348	8.674
expand_KEGG_edges	0.332	0.004	0.589
expand_KEGG_mappings	0.256	0.000	0.487
generate_mappings	0.000	0.000	0.001
get_KGML	0.248	0.000	0.935
get_drug_table	0.284	0.000	1.456
get_fisher_info	0.008	0.000	0.006
get_graph_object	6.092	0.024	6.374
node_mapping_info	0.176	0.000	0.410
overlap_info	15.436	0.376	16.074
path_genes_by_cell_type	6.444	0.036	6.705
refine_mappings	6.124	0.028	6.452