Zuguang Gu
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/simona |
| git_branch: devel |
| git_last_commit: 73a246f |
| git_last_commit_date: 2024-04-15 04:48:25 -0400 (Mon, 15 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:41:24 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 1983/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| simona 1.1.14 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: simona |
| Version: 1.1.14 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:simona.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings simona_1.1.14.tar.gz |
| StartedAt: 2024-04-29 10:34:52 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 10:37:36 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 164.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: simona.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:simona.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings simona_1.1.14.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/simona.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simona/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simona’ version ‘1.1.14’
* 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: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 16.0Mb
sub-directories of 1Mb or more:
libs 14.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create_ontology_DAG_from_GO_db 5.058 0.204 5.277
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/simona.Rcheck/00check.log’
for details.
simona.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL simona ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘simona’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c annotation.cpp -o annotation.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c common_ancestor.cpp -o common_ancestor.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dist.cpp -o dist.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c intersectToList_logical.cpp -o intersectToList_logical.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c partition.cpp -o partition.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c permutation.cpp -o permutation.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c plot.cpp -o plot.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c reorder.cpp -o reorder.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sim.cpp -o sim.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c term.cpp -o term.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c traverse.cpp -o traverse.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c tree.cpp -o tree.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)
simona.Rcheck/tests/test-all.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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)))
>
> 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 369 ]
>
> proc.time()
user system elapsed
45.607 1.116 46.837
simona.Rcheck/simona-Ex.timings
| name | user | system | elapsed | |
| all_methods | 0.000 | 0.000 | 0.001 | |
| annotation | 0.006 | 0.004 | 0.012 | |
| common_ancestor | 0.031 | 0.004 | 0.036 | |
| create_ontology_DAG | 0.019 | 0.000 | 0.019 | |
| create_ontology_DAG_from_GO_db | 5.058 | 0.204 | 5.277 | |
| dag_all_terms | 0.003 | 0.000 | 0.003 | |
| dag_as_igraph | 0.010 | 0.003 | 0.013 | |
| dag_depth | 0.004 | 0.000 | 0.003 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| dag_filter | 0.017 | 0.000 | 0.017 | |
| dag_longest_dist_to_offspring | 0.004 | 0.000 | 0.004 | |
| dag_random | 0.079 | 0.003 | 0.083 | |
| 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 | 0.007 | 0.000 | 0.007 | |
| dag_viz | 0 | 0 | 0 | |
| distance | 0.008 | 0.000 | 0.009 | |
| group_sim | 0.009 | 0.000 | 0.009 | |
| import_obo | 0 | 0 | 0 | |
| mcols_ontology_DAG | 0.018 | 0.000 | 0.018 | |
| method_param | 0 | 0 | 0 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| random_terms | 0.003 | 0.000 | 0.003 | |
| simona_opt | 0.002 | 0.000 | 0.003 | |
| subset | 0.021 | 0.000 | 0.021 | |
| term_IC | 0.004 | 0.000 | 0.004 | |
| term_sim | 0.006 | 0.000 | 0.007 | |