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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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

Package 1772/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.33.0  (landing page)
Michael Zimmermann
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/RITAN
git_branch: devel
git_last_commit: 0affcc6
git_last_commit_date: 2025-07-15 23:45:24 -0400 (Tue, 15 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for RITAN on kjohnson3

To the developers/maintainers of the RITAN package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RITAN
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RITAN_1.33.0.tar.gz
StartedAt: 2025-08-08 21:15:02 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:16:59 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 117.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RITAN.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RITAN_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RITAN.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.33.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
See ‘/Users/biocbuild/bbs-3.22-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 code 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' 'hash' '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 ... 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/RITAN.Rcheck/00check.log’
for details.


Installation output

RITAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RITAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RITAN’ ...
** this is package ‘RITAN’ version ‘1.33.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
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 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package can be loaded from final location
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.graph000
check_any_net_input1.0370.0201.069
check_net_input0.0170.0010.018
enrichment_symbols0.3520.0070.358
geneset_overlap0.0350.0020.037
icon_test000
load_geneset_symbols0.0050.0010.005
network_overlap0.0050.0000.006
plot.term_enrichment0.3630.1120.480
plot.term_enrichment_by_subset0.0070.0000.007
readGMT000
readSIF000
resource_reduce0.7540.0660.823
show_active_genesets_hist0.0070.0000.008
summary.term_enrichment0.3040.1170.429
summary.term_enrichment_by_subset1.0360.1941.255
term_enrichment0.2790.0960.392
term_enrichment_by_subset0.0050.0000.006
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes0.0000.0010.000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000