Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:36:55 -0400 (Sat, 04 May 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" | 4753 |
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" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1475/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.26.0 (landing page) Vincent Carey
| 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 | ERROR | skipped | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the ontoProc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.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: ontoProc |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ontoProc_1.26.0.tar.gz |
StartedAt: 2024-05-04 01:48:42 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 02:17:42 -0400 (Sat, 04 May 2024) |
EllapsedTime: 1740.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ontoProc_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.26.0’ * 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 ‘ontoProc’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: app 1.6Mb data 1.8Mb ontoRda 2.7Mb owl 3.0Mb * 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 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 ... NOTE CLfeat : prupdate: no visible binding for global variable ‘PROSYM’ CLfeat : prupdate: no visible binding for global variable ‘PRID’ CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’ ctmarks : server: no visible binding for global variable ‘text’ ctmarks : server: no visible binding for global variable ‘packDesc2022’ ctmarks : server: no visible binding for global variable ‘packDesc2021’ ctmarks: no visible binding for global variable ‘cumu’ dropStop: no visible binding for global variable ‘stopWords’ getOnto: no visible binding for global variable ‘rdatadateadded’ getOnto: no visible binding for global variable ‘title’ getOnto: no visible binding for global variable ‘description’ ldfToTerm: no visible binding for global variable ‘PROSYM’ sym2CellOnto: no visible binding for global variable ‘PROSYM’ sym2CellOnto: no visible binding for global variable ‘SYMBOL’ Undefined global functions or variables: PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022 rdatadateadded stopWords text title Consider adding importFrom("graphics", "text", "title") to your NAMESPACE file. * 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 ... NOTE S3 methods shown with full name in Rd file 'plot.owlents.Rd': ‘plot.owlents’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 162 marked UTF-8 strings * 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 sym2CellOnto 87.068 92.144 357.872 siblings_TAG 59.825 8.045 85.195 CLfeats 43.222 4.377 49.824 plot.owlents 26.343 19.238 54.958 owl2cache 22.532 7.148 85.674 nomenCheckup 27.061 1.830 36.782 getLeavesFromTerm 27.262 1.049 28.762 common_classes 22.539 2.044 29.782 fastGrep 22.125 1.269 25.736 secLevGen 16.551 1.435 20.698 onto_plot2 15.405 1.551 33.473 cleanCLOnames 14.734 0.968 16.057 make_graphNEL_from_ontology_plot 14.119 1.251 16.201 findCommonAncestors 14.161 1.207 15.766 TermSet-class 13.707 0.992 17.250 liberalMap 11.827 0.676 12.939 selectFromMap 10.257 1.483 14.788 ancestors 10.865 0.539 12.470 getOnto 10.381 0.776 11.510 mapOneNaive 8.328 0.928 9.557 parents 8.608 0.413 13.878 subclasses 7.744 0.823 11.453 children_names 6.911 0.254 7.689 ancestors_names 5.582 0.156 5.738 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘ontoProc’ ... ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ontoProc)
ontoProc.Rcheck/tests/test.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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(ontoProc) Loading required package: ontologyIndex > library(testthat) > > test_check("ontoProc") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > > proc.time() user system elapsed 115.642 20.016 230.389
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 43.222 | 4.377 | 49.824 | |
PROSYM | 0.502 | 0.003 | 0.506 | |
TermSet-class | 13.707 | 0.992 | 17.250 | |
allGOterms | 0.330 | 0.048 | 0.378 | |
ancestors | 10.865 | 0.539 | 12.470 | |
ancestors_names | 5.582 | 0.156 | 5.738 | |
cellTypeToGO | 2.861 | 0.165 | 3.176 | |
children_names | 6.911 | 0.254 | 7.689 | |
cleanCLOnames | 14.734 | 0.968 | 16.057 | |
common_classes | 22.539 | 2.044 | 29.782 | |
ctmarks | 0.001 | 0.000 | 0.001 | |
cyclicSigset | 0.011 | 0.002 | 0.014 | |
demoApp | 0.001 | 0.000 | 0.001 | |
dropStop | 0.008 | 0.000 | 0.008 | |
fastGrep | 22.125 | 1.269 | 25.736 | |
findCommonAncestors | 14.161 | 1.207 | 15.766 | |
getLeavesFromTerm | 27.262 | 1.049 | 28.762 | |
getOnto | 10.381 | 0.776 | 11.510 | |
humrna | 0.006 | 0.002 | 0.008 | |
ldfToTerms | 2.571 | 0.049 | 2.620 | |
liberalMap | 11.827 | 0.676 | 12.939 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 14.119 | 1.251 | 16.201 | |
mapOneNaive | 8.328 | 0.928 | 9.557 | |
minicorpus | 0.002 | 0.000 | 0.002 | |
nomenCheckup | 27.061 | 1.830 | 36.782 | |
onto_plot2 | 15.405 | 1.551 | 33.473 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 22.532 | 7.148 | 85.674 | |
packDesc2019 | 0.003 | 0.012 | 0.025 | |
packDesc2021 | 0.008 | 0.024 | 0.043 | |
packDesc2022 | 0.003 | 0.008 | 0.011 | |
packDesc2023 | 0.011 | 0.000 | 0.019 | |
parents | 8.608 | 0.413 | 13.878 | |
plot.owlents | 26.343 | 19.238 | 54.958 | |
recognizedPredicates | 0.001 | 0.000 | 0.001 | |
secLevGen | 16.551 | 1.435 | 20.698 | |
selectFromMap | 10.257 | 1.483 | 14.788 | |
setup_entities | 3.784 | 0.052 | 3.836 | |
seur3kTab | 0.003 | 0.003 | 0.009 | |
siblings_TAG | 59.825 | 8.045 | 85.195 | |
stopWords | 0.003 | 0.002 | 0.005 | |
subclasses | 7.744 | 0.823 | 11.453 | |
sym2CellOnto | 87.068 | 92.144 | 357.872 | |
valid_ontonames | 0.000 | 0.000 | 0.001 | |