Package: KEGGlincs

Version: 1.9.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGlincs_1.9.1.tar.gz

StartedAt: 2019-04-09 01:31:23 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:34:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 191.9 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGlincs_1.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/KEGGlincs.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.1’
* 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
add_edge_data           20.065  0.491  21.853
overlap_info            17.803  0.803  18.830
edge_mapping_info       10.442  0.235  10.910
refine_mappings          9.249  0.173   9.814
path_genes_by_cell_type  8.787  0.132   9.167
get_graph_object         7.022  0.052   7.299
* 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-3.9-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL KEGGlincs
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* installing to library ‘/home/biocbuild/bbs-3.9-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	0.000	0.000	0.001
KL_compare	0	0	0
add_edge_data	20.065	0.491	21.853
cyto_vis	0.505	0.000	0.736
edge_mapping_info	10.442	0.235	10.910
expand_KEGG_edges	0.407	0.017	0.657
expand_KEGG_mappings	0.189	0.000	0.408
generate_mappings	0.001	0.000	0.001
get_KGML	0.231	0.000	0.918
get_fisher_info	0.006	0.000	0.006
get_graph_object	7.022	0.052	7.299
keggerize_edges	0.001	0.000	0.000
node_mapping_info	0.185	0.000	0.399
overlap_info	17.803	0.803	18.830
path_genes_by_cell_type	8.787	0.132	9.167
refine_mappings	9.249	0.173	9.814
tidy_edge	0.001	0.000	0.000