BioC 3.5: CHECK report for KEGGlincs on oaxaca

Package: KEGGlincs

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGlincs_1.1.0.tar.gz

StartedAt: 2017-02-28 04:18:34 -0800 (Tue, 28 Feb 2017)

EndedAt: 2017-02-28 04:22:12 -0800 (Tue, 28 Feb 2017)

EllapsedTime: 218.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGlincs.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGlincs_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/KEGGlincs.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘XML’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
add_edge_data           21.381  1.355  23.888
overlap_info            15.653  1.498  17.341
add_kegg_drugs          10.656  0.320  14.770
edge_mapping_info       10.121  0.708  11.017
path_genes_by_cell_type  9.317  0.509  10.022
refine_mappings          7.933  0.483   8.693
get_graph_object         6.882  0.363   7.433
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGlincs’ ...
** R
** inst
** preparing 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	0.001	0.000	0.001
add_edge_data	21.381	1.355	23.888
add_kegg_drugs	10.656	0.320	14.770
cyto_vis	0.473	0.002	0.661
edge_mapping_info	10.121	0.708	11.017
expand_KEGG_edges	0.354	0.002	0.546
expand_KEGG_mappings	0.228	0.001	0.417
generate_mappings	0.001	0.000	0.001
get_KGML	0.177	0.001	0.759
get_drug_table	0.229	0.001	0.933
get_fisher_info	0.006	0.000	0.005
get_graph_object	6.882	0.363	7.433
node_mapping_info	0.168	0.001	0.345
overlap_info	15.653	1.498	17.341
path_genes_by_cell_type	9.317	0.509	10.022
refine_mappings	7.933	0.483	8.693