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This page was generated on 2024-03-28 11:38:23 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1755/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.27.0  (landing page)
Michael Zimmermann
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/RITAN
git_branch: devel
git_last_commit: 487e78f
git_last_commit_date: 2023-10-24 10:57:21 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for RITAN on palomino3


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: 1.27.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RITAN.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RITAN_1.27.0.tar.gz
StartedAt: 2024-03-28 05:56:45 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 06:02:55 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 369.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RITAN.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RITAN.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RITAN_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/RITAN.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RITAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RITAN' version '1.27.0'
* 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 whether package 'RITAN' can be installed ... WARNING
Found the following significant warnings:
  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 'F:/biocbuild/bbs-3.19-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' '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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plot.term_enrichment 1.89   0.53   88.67
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/RITAN.Rcheck/00check.log'
for details.


Installation output

RITAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL RITAN
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 '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 '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 '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.graph000
check_any_net_input2.050.092.17
check_net_input0.050.000.05
enrichment_symbols0.610.060.67
geneset_overlap0.090.000.09
icon_test000
load_geneset_symbols0.000.020.02
network_overlap0.030.000.03
plot.term_enrichment 1.89 0.5388.67
plot.term_enrichment_by_subset0.020.010.03
readGMT000
readSIF000
resource_reduce2.080.162.24
show_active_genesets_hist0.010.000.01
summary.term_enrichment0.680.501.16
summary.term_enrichment_by_subset1.210.862.08
term_enrichment0.600.441.03
term_enrichment_by_subset0.010.000.01
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000