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This page was generated on 2022-06-24 12:05:18 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RITAN on nebbiolo1


To the developers/maintainers of the RITAN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RITAN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1659/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.20.0  (landing page)
Michael Zimmermann
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/RITAN
git_branch: RELEASE_3_15
git_last_commit: 3d2e50b
git_last_commit_date: 2022-04-26 11:40:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: RITAN
Version: 1.20.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RITAN_1.20.0.tar.gz
StartedAt: 2022-06-23 21:41:31 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:45:57 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 265.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RITAN.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RITAN_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RITAN.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.20.0’
* 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 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'RITAN'
  Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
  Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
See ‘/home/biocbuild/bbs-3.15-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:
  ‘BgeeDB’
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
enrichment_symbols: no visible binding for global variable
  'active_genesets'
icon_dual_between: no visible binding for global variable 'all_symbols'
icon_single_within: no visible binding for global variable
  'all_symbols'
load_geneset_symbols: no visible binding for global variable
  'geneset_list'
load_geneset_symbols: no visible binding for global variable
  'active_genesets'
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_symbols geneset_list
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RITAN.Rcheck/00check.log’
for details.



Installation output

RITAN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RITAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘RITAN’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package keeps a record of temporary installation path
* DONE (RITAN)

Tests output


Example timings

RITAN.Rcheck/RITAN-Ex.timings

nameusersystemelapsed
as.graph0.0000.0000.001
check_any_net_input1.8070.1111.922
check_net_input0.0460.0000.046
enrichment_symbols1.4350.0851.529
geneset_overlap0.0970.0000.097
icon_test000
load_geneset_symbols0.0140.0000.013
network_overlap0.0180.0000.018
plot.term_enrichment0.7610.2350.999
plot.term_enrichment_by_subset0.0160.0000.016
readGMT000
readSIF0.0000.0000.001
resource_reduce2.0440.0722.116
show_active_genesets_hist0.0180.0000.018
summary.term_enrichment0.6610.1640.825
summary.term_enrichment_by_subset1.1170.4641.581
term_enrichment0.6150.1680.783
term_enrichment_by_subset0.0160.0000.016
vac1.day0vs31.de.genes0.0000.0000.001
vac1.day0vs56.de.genes0.0010.0000.000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT0.0000.0000.001
write_simple_table000