Package: KEGGlincs

Version: 1.9.1

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_1.9.1.tar.gz

StartedAt: 2019-04-09 01:47:13 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:50:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 224.0 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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/KEGGlincs.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.1’
* 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            21.809  2.072  24.587
add_edge_data           18.874  1.614  20.996
edge_mapping_info       10.559  0.753  11.600
path_genes_by_cell_type 10.352  0.708  11.360
refine_mappings          8.899  0.596   9.755
get_graph_object         8.706  0.304   9.316
* 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-3.9-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’ ...
** 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
* DONE (KEGGlincs)

name	user	system	elapsed
KEGG_lincs	0.000	0.000	0.001
KL_compare	0	0	0
add_edge_data	18.874	1.614	20.996
cyto_vis	0.578	0.025	0.832
edge_mapping_info	10.559	0.753	11.600
expand_KEGG_edges	0.490	0.049	0.763
expand_KEGG_mappings	0.196	0.005	0.461
generate_mappings	0.001	0.000	0.002
get_KGML	0.235	0.002	0.919
get_fisher_info	0.003	0.000	0.004
get_graph_object	8.706	0.304	9.316
keggerize_edges	0	0	0
node_mapping_info	0.311	0.007	0.570
overlap_info	21.809	2.072	24.587
path_genes_by_cell_type	10.352	0.708	11.360
refine_mappings	8.899	0.596	9.755
tidy_edge	0.001	0.000	0.000