Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ontoProc package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1311/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.14.0 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ontoProc |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoProc_1.14.0.tar.gz |
StartedAt: 2021-10-14 21:56:29 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:01:41 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 312.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoProc_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.14.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 41.5Mb sub-directories of 1Mb or more: app 1.9Mb data 2.0Mb ontoRda 37.1Mb * 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 ... 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 ‘PRID’ CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’ bind_formal_tags: no visible global function definition for ‘colData’ bind_formal_tags: no visible global function definition for ‘colData<-’ common_classes: no visible global function definition for ‘colData’ connect_classes: no visible global function definition for ‘colData’ ctmarks: no visible binding for '<<-' assignment to ‘pr’ ctmarks: no visible binding for '<<-' assignment to ‘go’ ctmarks : server: no visible binding for global variable ‘text’ ldfToTerm: no visible binding for global variable ‘PROSYM’ subset_descendants: no visible global function definition for ‘colData’ sym2CellOnto: no visible binding for global variable ‘SYMBOL’ Undefined global functions or variables: PRID PROSYM SYMBOL colData colData<- text Consider adding importFrom("graphics", "text") 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 LazyData ... OK * 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 common_classes 27.346 1.139 30.482 CLfeats 18.810 0.384 19.206 fastGrep 15.239 0.177 15.429 getLeavesFromTerm 11.102 0.101 11.386 sym2CellOnto 9.727 0.148 9.883 getCellOnto 6.596 0.067 6.666 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ontoProc’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 8 ] > > > proc.time() user system elapsed 28.250 0.752 29.008
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 18.810 | 0.384 | 19.206 | |
PROSYM | 0.002 | 0.000 | 0.002 | |
TermSet-class | 0.405 | 0.008 | 0.413 | |
allGOterms | 0.063 | 0.002 | 0.066 | |
cellTypeToGO | 2.444 | 0.151 | 2.598 | |
cleanCLOnames | 1.008 | 0.020 | 1.030 | |
common_classes | 27.346 | 1.139 | 30.482 | |
cyclicSigset | 0.014 | 0.000 | 0.014 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.005 | 0.001 | 0.007 | |
fastGrep | 15.239 | 0.177 | 15.429 | |
findCommonAncestors | 3.578 | 0.208 | 3.788 | |
getCellOnto | 6.596 | 0.067 | 6.666 | |
getLeavesFromTerm | 11.102 | 0.101 | 11.386 | |
humrna | 0.009 | 0.002 | 0.011 | |
ldfToTerms | 0.318 | 0.014 | 0.333 | |
liberalMap | 3.465 | 0.037 | 3.505 | |
makeSelectInput | 0.001 | 0.001 | 0.001 | |
make_graphNEL_from_ontology_plot | 2.952 | 0.018 | 2.971 | |
mapOneNaive | 2.558 | 0.020 | 2.579 | |
minicorpus | 0.002 | 0.002 | 0.004 | |
nomenCheckup | 1.198 | 0.019 | 1.218 | |
onto_plot2 | 3.034 | 0.030 | 3.065 | |
onto_roots | 0.001 | 0.001 | 0.001 | |
packDesc2019 | 0.003 | 0.001 | 0.003 | |
recognizedPredicates | 0.001 | 0.000 | 0.001 | |
secLevGen | 0.412 | 0.002 | 0.414 | |
selectFromMap | 2.834 | 0.019 | 2.854 | |
seur3kTab | 0.005 | 0.001 | 0.007 | |
siblings_TAG | 1.085 | 0.006 | 1.093 | |
stopWords | 0.002 | 0.001 | 0.004 | |
sym2CellOnto | 9.727 | 0.148 | 9.883 | |