Multiple platform build/check report for BioC 3.21 - CHECK results for simona on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 simona on kunpeng2

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: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2025-01-25 11:42:29 -0000 (Sat, 25 Jan 2025)

EndedAt: 2025-01-25 11:45:04 -0000 (Sat, 25 Jan 2025)

EllapsedTime: 155.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: simona.Rcheck

Warnings: 5

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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/simona.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘1.5.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/simona.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 5 WARNINGs, 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-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-devel_2024-11-24/site-library’
* installing *source* package ‘simona’ ...
** 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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/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/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-simona/00new/simona/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (simona)

Tests output

simona.Rcheck/tests/test-all.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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)))
Warning: program compiled against libxml 212 using older 211
> 
> 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 374 ]
> 
> proc.time()
   user  system elapsed 
 40.683   0.974  41.729

Example timings

simona.Rcheck/simona-Ex.timings

name	user	system	elapsed
all_methods	0.001	0.000	0.001
annotation	0.010	0.000	0.013
common_ancestor	0.034	0.000	0.034
create_ontology_DAG	0.018	0.000	0.018
create_ontology_DAG_from_GO_db	3.737	0.116	3.870
dag_all_terms	0.003	0.000	0.003
dag_as_igraph	0.015	0.000	0.015
dag_depth	0.004	0.000	0.003
dag_distinct_ancestors	0.005	0.000	0.005
dag_enrich_on_items	0.000	0.000	0.001
dag_enrich_on_offsprings	0	0	0
dag_enrich_on_offsprings_by_permutation	0	0	0
dag_filter	0.016	0.000	0.017
dag_longest_dist_to_offspring	0.003	0.000	0.004
dag_random	0.079	0.004	0.083
dag_reorder	0.005	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	0.007	0.000	0.007
dag_viz	0.000	0.000	0.001
distance	0.008	0.000	0.008
group_sim	0.009	0.000	0.009
import_obo	0	0	0
mcols_ontology_DAG	0.017	0.000	0.016
method_param	0.001	0.000	0.000
n_annotations	0.004	0.000	0.003
n_terms	0.003	0.000	0.003
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	0.003
subset	0.019	0.000	0.019
term_IC	0.004	0.000	0.004
term_sim	0.006	0.000	0.006