Package: KEGGlincs

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings KEGGlincs_1.12.0.tar.gz

StartedAt: 2020-04-15 03:21:15 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:25:09 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 234.0 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 --install=check:KEGGlincs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings KEGGlincs_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
overlap_info            19.158  1.987  21.468
add_edge_data           18.532  1.661  21.196
edge_mapping_info       11.298  0.866  12.624
path_genes_by_cell_type 11.272  0.826  12.387
refine_mappings         11.142  0.748  12.162
get_graph_object         8.822  0.320   9.410
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL KEGGlincs
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘KEGGlincs’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGGlincs)

name	user	system	elapsed
KEGG_lincs	0.000	0.000	0.001
KL_compare	0.000	0.000	0.001
add_edge_data	18.532	1.661	21.196
cyto_vis	0.420	0.007	0.798
edge_mapping_info	11.298	0.866	12.624
expand_KEGG_edges	0.422	0.046	0.672
expand_KEGG_mappings	0.148	0.000	0.345
generate_mappings	0.001	0.000	0.001
get_KGML	0.200	0.002	0.799
get_fisher_info	0.003	0.000	0.003
get_graph_object	8.822	0.320	9.410
keggerize_edges	0.001	0.000	0.000
node_mapping_info	0.216	0.002	0.417
overlap_info	19.158	1.987	21.468
path_genes_by_cell_type	11.272	0.826	12.387
refine_mappings	11.142	0.748	12.162
tidy_edge	0	0	0