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CHECK report for RITAN on malbec1

This page was generated on 2018-04-12 13:16:15 -0400 (Thu, 12 Apr 2018).

Package 1183/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.2.0
Michael Zimmermann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RITAN
Branch: RELEASE_3_6
Last Commit: 3e5ba38
Last Changed Date: 2017-10-30 12:41:29 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.



Installation output

RITAN.Rcheck/00install.out

* 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)

Tests output


Example timings

RITAN.Rcheck/RITAN-Ex.timings

nameusersystemelapsed
as.graph0.0040.0000.001
check_any_net_input1.2960.0361.419
check_net_input0.0200.0000.018
enrichment_symbols1.7840.0644.302
geneset_overlap0.1080.0000.108
icon_test000
load_geneset_symbols0.0080.0000.009
network_overlap0.0120.0000.012
plot.term_enrichment0.8160.0323.339
plot.term_enrichment_by_subset0.0160.0000.013
readGMT0.0000.0000.001
readSIF000
show_active_genesets_hist0.0160.0000.016
summary.term_enrichment0.8080.0163.048
summary.term_enrichment_by_subset1.4800.0405.931
term_enrichment0.7080.0122.928
term_enrichment_by_subset0.0120.0000.011
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes0.0040.0000.000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000