Package: RITAN

Version: 1.2.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RITAN_1.2.0.tar.gz

StartedAt: 2018-04-12 02:27:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:29:12 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 79.0 seconds

RetCode: 0

Status:  OK

CheckDir: RITAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RITAN_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/RITAN.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.2.0’
* 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 ‘RITAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘sqldf’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BgeeDB’ ‘dynamicTreeCut’ ‘gsubfn’
  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 ... NOTE
check_any_net_input: no visible binding for global variable
  ‘network_list’
enrichment_symbols: no visible binding for global variable
  ‘active_genesets’
icon_dual_between: no visible global function definition for ‘ss2’
icon_dual_between: no visible binding for global variable ‘all_symbols’
icon_dual_between: no visible binding for global variable ‘all_net’
icon_single_within: no visible global function definition for ‘ss2’
icon_single_within: no visible binding for global variable
  ‘all_symbols’
icon_single_within: no visible binding for global variable ‘all_net’
load_geneset_symbols: no visible binding for global variable
  ‘geneset_list’
load_geneset_symbols: no visible binding for global variable ‘f’
load_geneset_symbols: no visible binding for global variable
  ‘active_genesets’
network_overlap : <anonymous>: no visible binding for global variable
  ‘network_list’
network_overlap: no visible binding for global variable ‘network_list’
network_overlap : select_edges: no visible binding for global variable
  ‘network_list’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var2’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var1’
show_active_genesets_hist: no visible binding for global variable
  ‘active_genesets’
term_enrichment : process_source: no visible binding for global
  variable ‘active_genesets’
Undefined global functions or variables:
  Var1 Var2 active_genesets all_net all_symbols f geneset_list
  network_list ss2
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
summary.term_enrichment_by_subset 1.48   0.04   5.931
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/RITAN.Rcheck/00check.log’
for details.

* installing *source* package ‘RITAN’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RITAN)

name	user	system	elapsed
as.graph	0.004	0.000	0.001
check_any_net_input	1.296	0.036	1.419
check_net_input	0.020	0.000	0.018
enrichment_symbols	1.784	0.064	4.302
geneset_overlap	0.108	0.000	0.108
icon_test	0	0	0
load_geneset_symbols	0.008	0.000	0.009
network_overlap	0.012	0.000	0.012
plot.term_enrichment	0.816	0.032	3.339
plot.term_enrichment_by_subset	0.016	0.000	0.013
readGMT	0.000	0.000	0.001
readSIF	0	0	0
show_active_genesets_hist	0.016	0.000	0.016
summary.term_enrichment	0.808	0.016	3.048
summary.term_enrichment_by_subset	1.480	0.040	5.931
term_enrichment	0.708	0.012	2.928
term_enrichment_by_subset	0.012	0.000	0.011
vac1.day0vs31.de.genes	0	0	0
vac1.day0vs56.de.genes	0.004	0.000	0.000
vac2.day0vs31.de.genes	0	0	0
vac2.day0vs56.de.genes	0	0	0
writeGMT	0	0	0
write_simple_table	0	0	0