Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-18 11:38:01 -0400 (Mon, 18 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" | 4685 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" | 4423 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" | 4450 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" | 4361 |
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 1445/2257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.25.6 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | 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: 1.25.6 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ontoProc_1.25.6.tar.gz |
StartedAt: 2024-03-18 04:45:03 -0400 (Mon, 18 Mar 2024) |
EndedAt: 2024-03-18 04:52:33 -0400 (Mon, 18 Mar 2024) |
EllapsedTime: 449.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ontoProc.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ontoProc_1.25.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck' * using R Under development (unstable) (2024-03-06 r86056 ucrt) * using platform: x86_64-w64-mingw32 * 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 '1.25.6' * 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 10.0Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 2.9Mb * 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 '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: common_classes > ### Title: list and count samples with common ontological annotation in two > ### SEs > ### Aliases: common_classes > > ### ** Examples > > if (requireNamespace("celldex")) { + imm = celldex::ImmGenData() + if ("label.ont" %in% names(colData(imm))) { + cl = getOnto("cellOnto") + blu = celldex::BlueprintEncodeData() + common_classes( cl, imm, blu ) + } + } Loading required namespace: celldex Error in colData(imm) : could not find function "colData" Calls: %in% Execution halted * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck/00check.log' for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-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 Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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") * Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation [ FAIL 0 | WARN 12 | SKIP 0 | PASS 13 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 13 ] > > > proc.time() user system elapsed 89.75 6.82 102.76
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 30.84 | 2.94 | 49.91 | |
PROSYM | 0.20 | 0.00 | 0.21 | |
TermSet-class | 9.00 | 0.80 | 17.82 | |
allGOterms | 0.10 | 0.00 | 0.09 | |
ancestors | 16.92 | 1.14 | 20.44 | |
ancestors_names | 5.33 | 0.03 | 5.37 | |
cellTypeToGO | 1.76 | 0.29 | 2.06 | |
children_names | 6.66 | 0.11 | 6.78 | |
cleanCLOnames | 12.59 | 0.75 | 14.66 | |