Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:14 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz |
StartedAt: 2021-10-15 02:56:08 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 03:03:06 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 417.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 ... OK * checking for portable file names ... OK * checking whether package 'ontoProc' can be installed ... OK * checking installed package size ... NOTE installed size is 41.7Mb sub-directories of 1Mb or more: app 1.9Mb data 2.0Mb ontoRda 37.2Mb * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed common_classes 26.25 1.79 33.50 CLfeats 14.76 0.94 15.79 fastGrep 12.96 0.56 14.00 getLeavesFromTerm 8.58 0.11 8.69 sym2CellOnto 7.35 0.61 7.96 getCellOnto 5.39 0.08 5.50 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed common_classes 23.80 2.03 27.75 CLfeats 16.31 0.29 16.81 fastGrep 11.28 0.10 11.37 getLeavesFromTerm 10.30 0.03 10.32 sym2CellOnto 7.07 0.06 7.12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test.R' OK ** running tests for arch 'x64' ... 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck/00check.log' for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ontoProc_1.14.0.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.14.0.zip && rm ontoProc_1.14.0.tar.gz ontoProc_1.14.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 3 40.7M 3 1658k 0 0 1842k 0 0:00:22 --:--:-- 0:00:22 1842k 10 40.7M 10 4544k 0 0 2448k 0 0:00:17 0:00:01 0:00:16 2448k 20 40.7M 20 8512k 0 0 2982k 0 0:00:13 0:00:02 0:00:11 2982k 28 40.7M 28 11.5M 0 0 3059k 0 0:00:13 0:00:03 0:00:10 3059k 28 40.7M 28 11.5M 0 0 2430k 0 0:00:17 0:00:04 0:00:13 2430k 28 40.7M 28 11.6M 0 0 2029k 0 0:00:20 0:00:05 0:00:15 2062k 33 40.7M 33 13.6M 0 0 2044k 0 0:00:20 0:00:06 0:00:14 1894k 42 40.7M 42 17.1M 0 0 2241k 0 0:00:18 0:00:07 0:00:11 1818k 52 40.7M 52 21.4M 0 0 2478k 0 0:00:16 0:00:08 0:00:08 2027k 65 40.7M 65 26.6M 0 0 2768k 0 0:00:15 0:00:09 0:00:06 3100k 80 40.7M 80 32.7M 0 0 3089k 0 0:00:13 0:00:10 0:00:03 4335k 97 40.7M 97 39.7M 0 0 3429k 0 0:00:12 0:00:11 0:00:01 5326k 100 40.7M 100 40.7M 0 0 3461k 0 0:00:12 0:00:12 --:--:-- 5743k install for i386 Warning in untar2(tarfile, files, list, exdir, restore_times) : restoring symbolic link as a file copy * 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 converting help for package 'ontoProc' finding HTML links ... done CLfeats html PROSYM html TermSet-class html allGOterms html bind_formal_tags html c-TermSet-method html cellTypeToGO html cleanCLOnames html common_classes html connect_classes html ctmarks html cyclicSigset html demoApp html dropStop html fastGrep html findCommonAncestors html finding level-2 HTML links ... done getCellOnto html getLeavesFromTerm html humrna html improveNodes html ldfToTerms html liberalMap html makeSelectInput html make_graphNEL_from_ontology_plot html map2prose html mapOneNaive html minicorpus html nomenCheckup html onto_plot2 html onto_roots html packDesc2019 html recognizedPredicates html secLevGen html selectFromMap html seur3kTab html siblings_TAG html stopWords html subset_descendants html sym2CellOnto html ** 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 install for x64 Warning in untar2(tarfile, files, list, exdir, restore_times) : restoring symbolic link as a file copy * installing *source* package 'ontoProc' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ontoProc' as ontoProc_1.14.0.zip * DONE (ontoProc) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ontoProc' successfully unpacked and MD5 sums checked
ontoProc.Rcheck/tests_i386/test.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 5 | SKIP 0 | PASS 8 ] > > > proc.time() user system elapsed 22.40 1.07 23.45 |
ontoProc.Rcheck/tests_x64/test.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 5 | SKIP 0 | PASS 8 ] > > > proc.time() user system elapsed 20.21 0.65 20.84 |
ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings
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ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings
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