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This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 2017/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simona 1.7.1  (landing page)
Zuguang Gu
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/simona
git_branch: devel
git_last_commit: 6006862
git_last_commit_date: 2025-06-11 02:52:54 -0400 (Wed, 11 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for simona on taishan

To the developers/maintainers of the simona package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/simona.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: simona
Version: 1.7.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:simona.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings simona_1.7.1.tar.gz
StartedAt: 2025-10-17 13:42:36 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 13:45:21 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:   OK  
CheckDir: simona.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:simona.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings simona_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/simona.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simona/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simona’ version ‘1.7.1’
* package encoding: UTF-8
* 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 ‘simona’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'create_ontology_DAG_from_GO_db.Rd':
  ‘[org.Hs.eg.db:org.Hs.egBASE]{org.Hs.eg.db::org.Hs.eg.db}’

Non-topic package-anchored link(s) in Rd file 'create_ontology_DAG_from_igraph.Rd':
  ‘[igraph:aaa-igraph-package]{igraph::igraph}’

Non-topic package-anchored link(s) in Rd file 'dag_as_igraph.Rd':
  ‘[igraph:aaa-igraph-package]{igraph::igraph}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/simona.Rcheck/00check.log’
for details.

Installation output

simona.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL simona
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘simona’ ...
** this is package ‘simona’ version ‘1.7.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c annotation.cpp -o annotation.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c common_ancestor.cpp -o common_ancestor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c dist.cpp -o dist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c intersectToList_logical.cpp -o intersectToList_logical.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c partition.cpp -o partition.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c permutation.cpp -o permutation.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c plot.cpp -o plot.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c reorder.cpp -o reorder.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c sim.cpp -o sim.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c term.cpp -o term.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c traverse.cpp -o traverse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c tree.cpp -o tree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o simona.so RcppExports.o annotation.o common_ancestor.o dist.o intersectToList_logical.o partition.o permutation.o plot.o reorder.o sim.o term.o traverse.o tree.o utils.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-simona/00new/simona/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (simona)

Tests output

simona.Rcheck/tests/test-all.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(simona)))
> 
> test_check("simona")
GroupSim_pairwise_avg 
          group2
group1 0.4761502
GroupSim_pairwise_max 
       group2
group1      1
GroupSim_pairwise_BMA 
          group2
group1 0.7599716
GroupSim_pairwise_BMM 
          group2
group1 0.7955366
GroupSim_pairwise_ABM 
          group2
group1 0.7599716
GroupSim_pairwise_HDF 
          group2
group1 0.5866099
GroupSim_pairwise_MHDF 
          group2
group1 0.7244066
GroupSim_pairwise_VHDF 
          group2
group1 0.6986662
GroupSim_pairwise_Froehlich_2007 
          group2
group1 0.6614042
GroupSim_pairwise_Joeng_2014 
          group2
group1 0.7817037
GroupSim_SimALN 
          group2
group1 0.1512398
GroupSim_SimGIC 
          group2
group1 0.2697222
GroupSim_SimDIC 
          group2
group1 0.4248523
GroupSim_SimUIC 
          group2
group1 0.3693419
GroupSim_SimUI 
       group2
group1    0.2
GroupSim_SimDB 
          group2
group1 0.3333333
GroupSim_SimUB 
          group2
group1 0.3333333
GroupSim_SimNTO 
          group2
group1 0.3333333
GroupSim_SimCOU 
          group2
group1 0.4499397
GroupSim_SimCOT 
          group2
group1 0.2636391
GroupSim_SimLP 
       group2
group1      3
GroupSim_Ye_2005 
       group2
group1      1
GroupSim_SimCHO 
          group2
group1 0.6666667
GroupSim_SimALD 
       group2
group1   0.75
GroupSim_Jaccard 
       group2
group1   0.75
GroupSim_Dice 
          group2
group1 0.8571429
GroupSim_Overlap 
       group2
group1      1
GroupSim_Kappa 
          group2
group1 0.6666667
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 33.939   1.045  36.648

Example timings

simona.Rcheck/simona-Ex.timings

nameusersystemelapsed
all_methods0.0010.0000.001
annotation0.0100.0000.022
common_ancestor0.0310.0050.070
create_ontology_DAG0.0180.0000.035
create_ontology_DAG_from_GO_db3.5560.0834.513
dag_all_terms0.0030.0000.003
dag_as_igraph0.0150.0000.017
dag_depth0.0040.0000.004
dag_distinct_ancestors0.0050.0000.005
dag_enrich_on_items0.0000.0000.001
dag_enrich_on_offsprings000
dag_enrich_on_offsprings_by_permutation0.0010.0000.000
dag_filter0.0160.0000.016
dag_longest_dist_to_offspring0.0030.0000.003
dag_random0.0800.0000.081
dag_reorder0.0030.0030.006
dag_root0.0030.0000.002
dag_shiny0.0010.0000.000
dag_terms0.0030.0000.004
dag_treelize0.0070.0000.007
dag_viz0.0010.0000.000
distance0.0090.0000.008
group_sim0.0060.0040.009
import_obo0.0010.0000.000
mcols_ontology_DAG0.0180.0000.018
method_param000
n_annotations0.0040.0000.004
n_terms0.0040.0000.004
ontology_DAG-class0.0000.0000.001
partition_by_level000
random_terms0.0030.0000.003
simona_opt0.0030.0000.002
subset0.0190.0000.019
term_IC0.0040.0000.004
term_sim0.0060.0000.007