Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:37:04 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1460/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.24.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.24.0 |
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ontoProc_1.24.0.tar.gz |
StartedAt: 2024-04-16 03:25:31 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 03:35:53 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 622.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ontoProc_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.24.0' * 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 7.0Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb * 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 R 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 ... NOTE Namespace in Imports field not imported from: 'BiocFileCache' All declared Imports should be used. * 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 ... OK * 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 57.59 2.03 63.94 siblings_TAG 31.20 2.03 38.16 CLfeats 30.51 1.87 33.81 common_classes 18.91 2.93 23.50 getLeavesFromTerm 15.64 0.38 16.23 fastGrep 14.53 0.61 15.69 nomenCheckup 13.40 0.75 14.23 cleanCLOnames 13.37 0.63 14.23 TermSet-class 10.19 0.74 11.27 secLevGen 8.33 0.49 8.89 selectFromMap 7.80 0.76 8.66 make_graphNEL_from_ontology_plot 8.06 0.47 8.57 mapOneNaive 7.82 0.70 8.58 getOnto 7.95 0.56 8.63 onto_plot2 7.74 0.53 8.34 findCommonAncestors 7.58 0.65 8.31 liberalMap 7.32 0.56 8.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.18-bioc/meat/ontoProc.Rcheck/00check.log' for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 7 ] > > > proc.time() user system elapsed 77.84 5.57 90.14
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 30.51 | 1.87 | 33.81 | |
PROSYM | 0.22 | 0.00 | 0.22 | |
TermSet-class | 10.19 | 0.74 | 11.27 | |
allGOterms | 0.11 | 0.00 | 0.11 | |
cellTypeToGO | 1.67 | 0.12 | 1.82 | |
cleanCLOnames | 13.37 | 0.63 | 14.23 | |
common_classes | 18.91 | 2.93 | 23.50 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0 | 0 | 0 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0 | 0 | 0 | |
fastGrep | 14.53 | 0.61 | 15.69 | |
findCommonAncestors | 7.58 | 0.65 | 8.31 | |
getLeavesFromTerm | 15.64 | 0.38 | 16.23 | |
getOnto | 7.95 | 0.56 | 8.63 | |
humrna | 0.00 | 0.02 | 0.02 | |
ldfToTerms | 2.14 | 0.06 | 2.20 | |
liberalMap | 7.32 | 0.56 | 8.08 | |
makeSelectInput | 0 | 0 | 0 | |
make_graphNEL_from_ontology_plot | 8.06 | 0.47 | 8.57 | |
mapOneNaive | 7.82 | 0.70 | 8.58 | |
minicorpus | 0 | 0 | 0 | |
nomenCheckup | 13.40 | 0.75 | 14.23 | |
onto_plot2 | 7.74 | 0.53 | 8.34 | |
onto_roots | 0 | 0 | 0 | |
packDesc2019 | 0.01 | 0.00 | 0.02 | |
packDesc2021 | 0.00 | 0.02 | 0.01 | |
packDesc2022 | 0 | 0 | 0 | |
packDesc2023 | 0 | 0 | 0 | |
recognizedPredicates | 0 | 0 | 0 | |
secLevGen | 8.33 | 0.49 | 8.89 | |
selectFromMap | 7.80 | 0.76 | 8.66 | |
seur3kTab | 0.0 | 0.0 | 0.2 | |
siblings_TAG | 31.20 | 2.03 | 38.16 | |
stopWords | 0.00 | 0.02 | 0.01 | |
sym2CellOnto | 57.59 | 2.03 | 63.94 | |
valid_ontonames | 0 | 0 | 0 | |