Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1421/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.21.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
Package: ontoProc |
Version: 1.21.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ontoProc_1.21.0.tar.gz |
StartedAt: 2023-04-11 22:07:03 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 22:26:01 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 1138.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ontoProc_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ontoProc.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.21.0’ * 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 6.5Mb sub-directories of 1Mb or more: app 1.6Mb data 1.8Mb ontoRda 2.7Mb * 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 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 ... 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 CLfeats 33.465 2.622 37.359 siblings_TAG 29.508 3.086 51.421 getCellOnto 29.837 2.493 37.360 fastGrep 29.152 1.055 36.192 getLeavesFromTerm 22.088 1.410 30.757 sym2CellOnto 17.253 1.177 34.692 getOnto 16.602 1.146 27.059 selectFromMap 15.843 1.523 23.734 common_classes 13.870 0.879 16.174 mapOneNaive 13.580 1.092 17.328 liberalMap 13.336 0.855 19.375 TermSet-class 10.416 0.868 12.243 secLevGen 8.398 0.732 11.973 nomenCheckup 6.840 0.856 9.357 ldfToTerms 4.941 0.095 6.621 * 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 ... ‘ontoProc.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154) Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 9 | SKIP 0 | PASS 8 ] [ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ] > > > proc.time() user system elapsed 100.025 15.929 225.649
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 33.465 | 2.622 | 37.359 | |
PROSYM | 0.372 | 0.004 | 0.376 | |
TermSet-class | 10.416 | 0.868 | 12.243 | |
allGOterms | 0.184 | 0.003 | 0.187 | |
cellTypeToGO | 4.377 | 0.336 | 4.715 | |
cleanCLOnames | 3.987 | 0.563 | 4.912 | |
common_classes | 13.870 | 0.879 | 16.174 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.013 | 0.000 | 0.012 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.007 | 0.000 | 0.007 | |
fastGrep | 29.152 | 1.055 | 36.192 | |
findCommonAncestors | 4.451 | 0.244 | 4.696 | |
getCellOnto | 29.837 | 2.493 | 37.360 | |
getLeavesFromTerm | 22.088 | 1.410 | 30.757 | |
getOnto | 16.602 | 1.146 | 27.059 | |
humrna | 0.014 | 0.000 | 0.014 | |
ldfToTerms | 4.941 | 0.095 | 6.621 | |
liberalMap | 13.336 | 0.855 | 19.375 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 3.328 | 0.104 | 3.636 | |
mapOneNaive | 13.580 | 1.092 | 17.328 | |
minicorpus | 0.005 | 0.000 | 0.019 | |
nomenCheckup | 6.840 | 0.856 | 9.357 | |
onto_plot2 | 3.376 | 0.236 | 3.613 | |
onto_roots | 0.001 | 0.000 | 0.001 | |
packDesc2019 | 0.005 | 0.000 | 0.006 | |
packDesc2021 | 0.004 | 0.001 | 0.004 | |
packDesc2022 | 0.004 | 0.000 | 0.004 | |
recognizedPredicates | 0.000 | 0.001 | 0.001 | |
secLevGen | 8.398 | 0.732 | 11.973 | |
selectFromMap | 15.843 | 1.523 | 23.734 | |
seur3kTab | 0.006 | 0.000 | 0.006 | |
siblings_TAG | 29.508 | 3.086 | 51.421 | |
stopWords | 0.003 | 0.000 | 0.004 | |
sym2CellOnto | 17.253 | 1.177 | 34.692 | |
valid_ontonames | 0.000 | 0.000 | 0.001 | |