BioC 3.4: CHECK report for KEGGlincs on malbec1

Package: KEGGlincs

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings KEGGlincs_1.0.0.tar.gz

StartedAt: 2017-04-14 23:26:55 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:29:37 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 161.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings KEGGlincs_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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           16.616  0.284  18.030
overlap_info            14.656  0.220  15.115
edge_mapping_info        9.180  0.076   9.512
path_genes_by_cell_type  9.016  0.084   9.352
refine_mappings          7.420  0.064   7.796
get_graph_object         6.444  0.012   6.709
* 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_edge_data	16.616	0.284	18.030
cyto_vis	0.396	0.000	0.630
edge_mapping_info	9.180	0.076	9.512
expand_KEGG_edges	0.296	0.000	0.547
expand_KEGG_mappings	0.328	0.000	0.579
generate_mappings	0.000	0.000	0.001
get_KGML	0.272	0.004	0.997
get_fisher_info	0.004	0.000	0.004
get_graph_object	6.444	0.012	6.709
node_mapping_info	0.184	0.000	0.432
overlap_info	14.656	0.220	15.115
path_genes_by_cell_type	9.016	0.084	9.352
refine_mappings	7.420	0.064	7.796