Package: KEGGlincs

Version: 1.6.2

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings KEGGlincs_1.6.2.tar.gz

StartedAt: 2018-10-16 01:28:31 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:30:58 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 147.4 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGlincs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings KEGGlincs_1.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.2’
* 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           15.284  0.424  16.758
overlap_info            14.960  0.564  15.781
edge_mapping_info        8.420  0.292   8.979
path_genes_by_cell_type  7.652  0.184   8.102
refine_mappings          6.912  0.160   7.371
get_graph_object         6.072  0.016   6.345
* 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-3.7-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL KEGGlincs
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	0.004	0.000	0.001
KL_compare	0	0	0
add_edge_data	15.284	0.424	16.758
cyto_vis	0.352	0.000	0.591
edge_mapping_info	8.420	0.292	8.979
expand_KEGG_edges	0.304	0.012	0.572
expand_KEGG_mappings	0.168	0.000	0.430
generate_mappings	0.000	0.000	0.001
get_KGML	0.204	0.000	0.943
get_fisher_info	0.004	0.000	0.005
get_graph_object	6.072	0.016	6.345
keggerize_edges	0.004	0.000	0.001
node_mapping_info	0.208	0.004	0.447
overlap_info	14.960	0.564	15.781
path_genes_by_cell_type	7.652	0.184	8.102
refine_mappings	6.912	0.160	7.371
tidy_edge	0.004	0.000	0.000