Zuguang Gu
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2023/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| simona 1.7.1 (landing page) Zuguang Gu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. |
| Package: simona |
| Version: 1.7.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:simona.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings simona_1.7.1.tar.gz |
| StartedAt: 2025-10-24 00:14:23 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 00:16:53 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 150.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: simona.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:simona.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings simona_1.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/simona.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 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
‘/Users/biocbuild/bbs-3.22-bioc/meat/simona.Rcheck/00check.log’
for details.
simona.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL simona
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘simona’ ...
** this is package ‘simona’ version ‘1.7.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c annotation.cpp -o annotation.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c common_ancestor.cpp -o common_ancestor.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dist.cpp -o dist.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intersectToList_logical.cpp -o intersectToList_logical.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c partition.cpp -o partition.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c permutation.cpp -o permutation.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plot.cpp -o plot.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.cpp -o reorder.o
reorder.cpp:284:9: warning: variable 'total_force_diff' set but not used [-Wunused-but-set-variable]
double total_force_diff = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sim.cpp -o sim.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c term.cpp -o term.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c traverse.cpp -o traverse.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tree.cpp -o tree.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
simona.Rcheck/tests/test-all.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
34.374 3.231 37.834
simona.Rcheck/simona-Ex.timings
| name | user | system | elapsed | |
| all_methods | 0.000 | 0.001 | 0.002 | |
| annotation | 0.009 | 0.002 | 0.011 | |
| common_ancestor | 0.029 | 0.004 | 0.033 | |
| create_ontology_DAG | 0.014 | 0.002 | 0.016 | |
| create_ontology_DAG_from_GO_db | 3.475 | 0.140 | 3.631 | |
| dag_all_terms | 0.002 | 0.000 | 0.003 | |
| dag_as_igraph | 0.014 | 0.001 | 0.015 | |
| dag_depth | 0.004 | 0.001 | 0.005 | |
| dag_distinct_ancestors | 0.005 | 0.000 | 0.004 | |
| dag_enrich_on_items | 0 | 0 | 0 | |
| dag_enrich_on_offsprings | 0 | 0 | 0 | |
| dag_enrich_on_offsprings_by_permutation | 0 | 0 | 0 | |
| dag_filter | 0.010 | 0.001 | 0.012 | |
| dag_longest_dist_to_offspring | 0.002 | 0.001 | 0.003 | |
| dag_random | 0.073 | 0.003 | 0.078 | |
| dag_reorder | 0.006 | 0.000 | 0.006 | |
| dag_root | 0.003 | 0.000 | 0.003 | |
| dag_shiny | 0 | 0 | 0 | |
| dag_terms | 0.003 | 0.000 | 0.003 | |
| dag_treelize | 0.006 | 0.000 | 0.006 | |
| dag_viz | 0.001 | 0.000 | 0.001 | |
| distance | 0.006 | 0.001 | 0.008 | |
| group_sim | 0.007 | 0.000 | 0.008 | |
| import_obo | 0 | 0 | 0 | |
| mcols_ontology_DAG | 0.012 | 0.001 | 0.012 | |
| method_param | 0 | 0 | 0 | |
| n_annotations | 0.004 | 0.001 | 0.004 | |
| n_terms | 0.004 | 0.001 | 0.004 | |
| ontology_DAG-class | 0 | 0 | 0 | |
| partition_by_level | 0 | 0 | 0 | |
| random_terms | 0.003 | 0.000 | 0.003 | |
| simona_opt | 0.002 | 0.000 | 0.002 | |
| subset | 0.015 | 0.001 | 0.016 | |
| term_IC | 0.003 | 0.000 | 0.003 | |
| term_sim | 0.005 | 0.000 | 0.005 | |