Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-10 11:36:14 -0400 (Fri, 10 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" | 4515 |
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 | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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: 2024-05-10 01:14:47 -0400 (Fri, 10 May 2024) |
EndedAt: 2024-05-10 01:40:19 -0400 (Fri, 10 May 2024) |
EllapsedTime: 1531.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ontoProc.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 (2024-04-24) * 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 ... ERROR Running examples in ‘ontoProc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: sym2CellOnto > ### Title: use Cell Ontology and Protein Ontology to identify cell-type > ### defining conditions in which a given gene is named > ### Aliases: sym2CellOnto > > ### ** Examples > > if (!exists("cl")) cl = getOnto("cellOnto") loading from cache > if (!exists("pr")) pr = getOnto("PROnto") loading from cache Killed * 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: 1 ERROR, 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 (2024-04-24) -- "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 120.763 21.303 247.328
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 37.594 | 3.019 | 42.039 | |
PROSYM | 0.240 | 0.004 | 0.244 | |
TermSet-class | 15.366 | 1.014 | 18.754 | |
allGOterms | 0.235 | 0.024 | 0.259 | |
ancestors | 15.369 | 1.077 | 17.539 | |
ancestors_names | 6.815 | 0.337 | 7.732 | |
cellTypeToGO | 2.464 | 0.193 | 3.282 | |
children_names | 5.074 | 0.291 | 5.391 | |
cleanCLOnames | 18.559 | 1.168 | 20.059 | |
common_classes | 15.871 | 1.379 | 18.772 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.01 | 0.00 | 0.01 | |
demoApp | 0.000 | 0.000 | 0.001 | |
dropStop | 0.005 | 0.000 | 0.006 | |
fastGrep | 24.080 | 1.627 | 26.240 | |
findCommonAncestors | 10.050 | 0.965 | 11.308 | |
getLeavesFromTerm | 30.456 | 1.531 | 37.606 | |
getOnto | 12.064 | 1.082 | 16.570 | |
humrna | 0.006 | 0.008 | 0.012 | |
ldfToTerms | 2.970 | 0.057 | 3.027 | |
liberalMap | 15.886 | 0.817 | 19.926 | |
makeSelectInput | 0.001 | 0.000 | 0.000 | |
make_graphNEL_from_ontology_plot | 9.068 | 0.661 | 10.086 | |
mapOneNaive | 10.499 | 0.534 | 11.486 | |
minicorpus | 0.003 | 0.000 | 0.003 | |
nomenCheckup | 21.372 | 0.896 | 27.169 | |
onto_plot2 | 17.301 | 0.802 | 27.340 | |
onto_roots | 0.001 | 0.000 | 0.001 | |
owl2cache | 23.256 | 1.566 | 26.215 | |
packDesc2019 | 0.010 | 0.000 | 0.009 | |
packDesc2021 | 0.006 | 0.000 | 0.006 | |
packDesc2022 | 0.007 | 0.000 | 0.007 | |
packDesc2023 | 0.004 | 0.002 | 0.007 | |
parents | 6.776 | 0.184 | 6.971 | |
plot.owlents | 24.868 | 1.447 | 24.876 | |
recognizedPredicates | 0 | 0 | 0 | |
secLevGen | 17.125 | 1.219 | 28.664 | |
selectFromMap | 16.515 | 0.877 | 28.411 | |
setup_entities | 8.990 | 0.492 | 16.485 | |
seur3kTab | 0.007 | 0.004 | 0.024 | |
siblings_TAG | 51.436 | 4.972 | 71.362 | |
stopWords | 0.003 | 0.000 | 0.004 | |
subclasses | 8.791 | 0.299 | 10.171 | |