Package: KEGGlincs

Version: 1.12.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings KEGGlincs_1.12.0.tar.gz

StartedAt: 2020-04-15 04:14:44 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:18:22 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 217.9 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings KEGGlincs_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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            20.768  0.796  21.814
add_edge_data           20.032  0.568  21.525
edge_mapping_info       12.748  0.368  13.344
path_genes_by_cell_type 12.048  0.176  12.466
refine_mappings         11.048  0.184  11.540
get_graph_object         9.220  0.076   9.529
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL KEGGlincs
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	0	0
KL_compare	0	0	0
add_edge_data	20.032	0.568	21.525
cyto_vis	0.524	0.000	0.733
edge_mapping_info	12.748	0.368	13.344
expand_KEGG_edges	0.424	0.016	0.645
expand_KEGG_mappings	0.200	0.000	0.407
generate_mappings	0.000	0.000	0.001
get_KGML	0.248	0.004	0.866
get_fisher_info	0.004	0.000	0.006
get_graph_object	9.220	0.076	9.529
keggerize_edges	0	0	0
node_mapping_info	0.200	0.000	0.402
overlap_info	20.768	0.796	21.814
path_genes_by_cell_type	12.048	0.176	12.466
refine_mappings	11.048	0.184	11.540
tidy_edge	0	0	0