Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:58 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 | ERROR | ERROR | skipped | 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ontoProc_1.26.0.tar.gz |
StartedAt: 2024-05-22 04:45:05 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 04:57:35 -0400 (Wed, 22 May 2024) |
EllapsedTime: 749.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ontoProc_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 whether package 'ontoProc' can be installed ... OK * checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 2.9Mb * 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 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 55.00 2.61 71.63 CLfeats 30.61 2.42 45.41 siblings_TAG 28.31 2.39 30.92 plot.owlents 23.39 0.47 24.92 owl2cache 19.37 0.52 20.80 nomenCheckup 17.98 0.79 18.91 ancestors 14.42 1.17 18.08 fastGrep 14.45 1.11 21.91 common_classes 13.06 1.39 16.20 getLeavesFromTerm 13.35 0.96 14.48 secLevGen 12.47 0.94 15.80 cleanCLOnames 11.58 0.99 13.98 onto_plot2 10.66 0.83 13.73 selectFromMap 10.50 0.86 12.54 TermSet-class 9.65 0.83 13.36 make_graphNEL_from_ontology_plot 8.85 0.79 9.72 findCommonAncestors 8.59 0.78 9.44 liberalMap 8.33 0.94 9.29 getOnto 8.06 0.81 8.91 mapOneNaive 7.59 0.79 8.44 subclasses 7.05 0.14 7.39 parents 6.17 0.03 6.25 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck/00check.log' for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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") * Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > > proc.time() user system elapsed 89.12 6.56 97.64
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 30.61 | 2.42 | 45.41 | |
PROSYM | 0.19 | 0.03 | 0.22 | |
TermSet-class | 9.65 | 0.83 | 13.36 | |
allGOterms | 0.10 | 0.00 | 0.09 | |
ancestors | 14.42 | 1.17 | 18.08 | |
ancestors_names | 4.17 | 0.19 | 4.36 | |
cellTypeToGO | 2.33 | 0.07 | 2.53 | |
children_names | 4.01 | 0.05 | 4.07 | |
cleanCLOnames | 11.58 | 0.99 | 13.98 | |
common_classes | 13.06 | 1.39 | 16.20 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0 | 0 | 0 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.00 | 0.01 | 0.01 | |
fastGrep | 14.45 | 1.11 | 21.91 | |
findCommonAncestors | 8.59 | 0.78 | 9.44 | |
getLeavesFromTerm | 13.35 | 0.96 | 14.48 | |
getOnto | 8.06 | 0.81 | 8.91 | |
humrna | 0.00 | 0.01 | 0.01 | |
ldfToTerms | 2.44 | 0.02 | 2.46 | |
liberalMap | 8.33 | 0.94 | 9.29 | |
makeSelectInput | 0.01 | 0.00 | 0.02 | |
make_graphNEL_from_ontology_plot | 8.85 | 0.79 | 9.72 | |
mapOneNaive | 7.59 | 0.79 | 8.44 | |
minicorpus | 0 | 0 | 0 | |
nomenCheckup | 17.98 | 0.79 | 18.91 | |
onto_plot2 | 10.66 | 0.83 | 13.73 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 19.37 | 0.52 | 20.80 | |
packDesc2019 | 0.00 | 0.01 | 0.01 | |
packDesc2021 | 0.02 | 0.00 | 0.02 | |
packDesc2022 | 0.01 | 0.00 | 0.01 | |
packDesc2023 | 0.00 | 0.00 | 0.02 | |
parents | 6.17 | 0.03 | 6.25 | |
plot.owlents | 23.39 | 0.47 | 24.92 | |
recognizedPredicates | 0 | 0 | 0 | |
secLevGen | 12.47 | 0.94 | 15.80 | |
selectFromMap | 10.50 | 0.86 | 12.54 | |
setup_entities | 4.83 | 0.06 | 4.91 | |
seur3kTab | 0 | 0 | 0 | |
siblings_TAG | 28.31 | 2.39 | 30.92 | |
stopWords | 0 | 0 | 0 | |
subclasses | 7.05 | 0.14 | 7.39 | |
sym2CellOnto | 55.00 | 2.61 | 71.63 | |
valid_ontonames | 0 | 0 | 0 | |