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CHECK report for RITAN on merida1

This page was generated on 2019-04-16 12:00:39 -0400 (Tue, 16 Apr 2019).

Package 1316/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.6.0
Michael Zimmermann
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RITAN
Branch: RELEASE_3_8
Last Commit: 581a092
Last Changed Date: 2018-10-30 11:42:05 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RITAN
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RITAN_1.6.0.tar.gz
StartedAt: 2019-04-16 02:23:53 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:25:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 117.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RITAN.Rcheck
Warnings: 2

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RITAN_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’
  Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’
  Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’
  Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BgeeDB’ ‘knitr’
  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 ... WARNING
Documented arguments not in \usage in documentation object 'resource_reduce':
  ‘mutual_overlap’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
enrichment_symbols                2.044  0.098   6.377
summary.term_enrichment_by_subset 1.693  0.118   9.635
plot.term_enrichment              1.335  0.103   5.353
summary.term_enrichment           0.925  0.064   5.466
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck/00check.log’
for details.



Installation output

RITAN.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RITAN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RITAN’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’
Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’
Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’
* DONE (RITAN)

Tests output


Example timings

RITAN.Rcheck/RITAN-Ex.timings

nameusersystemelapsed
as.graph000
check_any_net_input1.8360.0911.935
check_net_input0.0840.0070.090
enrichment_symbols2.0440.0986.377
geneset_overlap0.1680.0110.180
icon_test000
load_geneset_symbols0.0070.0010.007
network_overlap0.0170.0010.019
plot.term_enrichment1.3350.1035.353
plot.term_enrichment_by_subset0.0170.0010.018
readGMT0.0010.0000.001
readSIF000
resource_reduce4.5790.1844.810
show_active_genesets_hist0.0180.0010.020
summary.term_enrichment0.9250.0645.466
summary.term_enrichment_by_subset1.6930.1189.635
term_enrichment0.9600.0644.664
term_enrichment_by_subset0.0150.0000.015
vac1.day0vs31.de.genes0.0010.0010.001
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes0.0000.0000.001
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table0.0000.0000.001