Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:24 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 rols package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rols.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1717/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rols 2.26.0 (landing page) Laurent Gatto
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: rols |
Version: 2.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rols_2.26.0.tar.gz |
StartedAt: 2023-04-10 22:20:16 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:31:34 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 677.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rols.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rols_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/rols.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘2.26.0’ * 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 ‘rols’ can be installed ... OK * checking installed package size ... OK * 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Term-class 47.123 1.666 255.447 CVParam-class 0.383 0.030 17.353 Ontology-class 0.295 0.014 6.322 Properties-class 0.287 0.010 5.421 OlsSearch-class 0.179 0.012 8.523 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘rols’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘lapply’ from package ‘base’ in package ‘rols’ ** 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 (rols)
rols.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > library("testthat") > library("rols") This is 'rols' version 2.26.0 > > test_check("rols") [, , Hello, World] Object of class 'OlsSearch': ontolgy: GO query: cell requested: 20 (out of 4093) response(s): 0 Object of class 'Ontologies' with 280 entries RS, SBO ... T4FS, CPONT Object of class 'Ontologies' with 1 entries RS Object of class 'Ontologies' with 2 entries RS, SBO Object of class 'Ontologies' with 3 entries RS, SBO, SCDO Object of class 'Ontologies' with 4 entries RS, SBO, SCDO, SDGIO Object of class 'Ontologies' with 5 entries RS, SBO ... SDGIO, SEPIO Ontology: Gene Ontology (go) The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. Loaded: 2023-01-04 Updated: 2023-01-04 Version: 2022-12-04 51052 terms 68 properties 0 individuals Object of class 'Properties' with 92 entries From the SO ontology partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR Object of class 'Properties' with 147 entries From the UBERON ontology digestive system gland, abdomen element ... liver lobule, bile A Property from the UBERON ontology: UBERON:0006925 Label: digestive system gland Object of class 'Terms' with 2729 entries From the SO ontology SO:0000579, SO:0000833 ... SO:0000071, SO:0000070 Object of class 'Terms' with 1 entries From the SO ontology SO:0000579 Object of class 'Terms' with 2 entries From the SO ontology SO:0000579, SO:0000833 Object of class 'Terms' with 3 entries From the SO ontology SO:0000579, SO:0000833, SO:0000578 Object of class 'Terms' with 4 entries From the SO ontology SO:0000579, SO:0000833, SO:0000578, SO:0000011 Object of class 'Terms' with 5 entries From the SO ontology SO:0000579, SO:0000833 ... SO:0000011, SO:0001430 A Term from the GO ontology: GO:0032801 Label: receptor catabolic process No description Testing term SO:0100015 Testing term SO:1001191 Testing term SO:0000248 Testing term SO:0000172 Testing term SO:0001185 Testing term SO:0001259 Testing term SO:0000783 Testing term SO:0000214 Testing term SO:0000579 Testing term SO:1000008 [ FAIL 0 | WARN 0 | SKIP 1 | PASS 194 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 194 ] > > proc.time() user system elapsed 44.624 1.035 340.696
rols.Rcheck/rols-Ex.timings
name | user | system | elapsed | |
CVParam-class | 0.383 | 0.030 | 17.353 | |
OlsSearch-class | 0.179 | 0.012 | 8.523 | |
Ontology-class | 0.295 | 0.014 | 6.322 | |
Properties-class | 0.287 | 0.010 | 5.421 | |
Term-class | 47.123 | 1.666 | 255.447 | |