Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:49 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1456/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.25.8 (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 | ||||||||||
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: 1.25.8 |
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_1.25.8.tar.gz |
StartedAt: 2024-03-28 00:56:12 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 01:20:55 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 1483.1 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_1.25.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘1.25.8’ * 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 81.254 6.080 132.984 CLfeats 47.586 4.910 55.491 siblings_TAG 41.205 5.936 101.757 nomenCheckup 29.876 3.847 45.438 owl2cache 27.996 2.444 34.780 plot.owlents 24.012 1.702 25.529 cleanCLOnames 23.662 1.749 28.731 fastGrep 21.646 1.556 24.317 make_graphNEL_from_ontology_plot 20.560 1.567 28.723 getLeavesFromTerm 19.732 1.709 22.653 secLevGen 18.899 1.962 24.920 mapOneNaive 18.903 1.933 27.868 selectFromMap 17.176 3.008 29.857 liberalMap 17.396 1.411 24.062 common_classes 15.593 2.112 19.054 ancestors 16.571 0.944 18.896 subclasses 13.661 3.081 46.261 findCommonAncestors 13.208 1.145 15.214 TermSet-class 10.194 1.111 11.683 parents 9.804 0.903 15.809 onto_plot2 9.520 1.054 11.005 getOnto 8.965 0.936 10.232 children_names 7.954 0.066 8.190 setup_entities 7.484 0.390 8.304 ancestors_names 5.017 0.124 5.142 ldfToTerms 4.892 0.176 5.074 * 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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 136.945 12.416 174.608
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 47.586 | 4.910 | 55.491 | |
PROSYM | 0.258 | 0.020 | 0.278 | |
TermSet-class | 10.194 | 1.111 | 11.683 | |
allGOterms | 0.121 | 0.004 | 0.135 | |
ancestors | 16.571 | 0.944 | 18.896 | |
ancestors_names | 5.017 | 0.124 | 5.142 | |
cellTypeToGO | 1.541 | 0.108 | 1.648 | |
children_names | 7.954 | 0.066 | 8.190 | |
cleanCLOnames | 23.662 | 1.749 | 28.731 | |
common_classes | 15.593 | 2.112 | 19.054 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.004 | 0.003 | 0.007 | |
demoApp | 0.001 | 0.000 | 0.000 | |
dropStop | 0.002 | 0.003 | 0.004 | |
fastGrep | 21.646 | 1.556 | 24.317 | |
findCommonAncestors | 13.208 | 1.145 | 15.214 | |
getLeavesFromTerm | 19.732 | 1.709 | 22.653 | |
getOnto | 8.965 | 0.936 | 10.232 | |
humrna | 0.011 | 0.004 | 0.015 | |
ldfToTerms | 4.892 | 0.176 | 5.074 | |
liberalMap | 17.396 | 1.411 | 24.062 | |
makeSelectInput | 0.000 | 0.001 | 0.002 | |
make_graphNEL_from_ontology_plot | 20.560 | 1.567 | 28.723 | |
mapOneNaive | 18.903 | 1.933 | 27.868 | |
minicorpus | 0.002 | 0.002 | 0.018 | |
nomenCheckup | 29.876 | 3.847 | 45.438 | |
onto_plot2 | 9.520 | 1.054 | 11.005 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 27.996 | 2.444 | 34.780 | |
packDesc2019 | 0.002 | 0.009 | 0.018 | |
packDesc2021 | 0.009 | 0.000 | 0.049 | |
packDesc2022 | 0.006 | 0.002 | 0.008 | |
packDesc2023 | 0.008 | 0.000 | 0.039 | |
parents | 9.804 | 0.903 | 15.809 | |
plot.owlents | 24.012 | 1.702 | 25.529 | |
recognizedPredicates | 0.000 | 0.001 | 0.000 | |
secLevGen | 18.899 | 1.962 | 24.920 | |
selectFromMap | 17.176 | 3.008 | 29.857 | |
setup_entities | 7.484 | 0.390 | 8.304 | |
seur3kTab | 0.004 | 0.000 | 0.004 | |
siblings_TAG | 41.205 | 5.936 | 101.757 | |
stopWords | 0.000 | 0.003 | 0.015 | |
subclasses | 13.661 | 3.081 | 46.261 | |
sym2CellOnto | 81.254 | 6.080 | 132.984 | |
valid_ontonames | 0.001 | 0.000 | 0.001 | |