Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:49 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 1708/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rols 2.27.0 (landing page) Laurent Gatto
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
Package: rols |
Version: 2.27.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rols_2.27.0.tar.gz |
StartedAt: 2023-02-28 13:37:00 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 14:17:00 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 2400.2 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: rols.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rols_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rols.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-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 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘2.27.0’ * 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 ... ERROR Running examples in ‘rols-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Term-class > ### Title: Class '"Term"' > ### Aliases: Term class:Term Term-class Terms class:Terms Terms-class > ### termLabel termLabel,Term-method termLabel,Terms-method termNamespace > ### termNamespace,Term-method termNamespace,Terms-method termOntology > ### termOntology,Term-method termOntology,Terms-method termSynonym > ### termSynonym,Term-method termSynonym,Terms-method termDesc > ### termDesc,Term-method termDesc,Terms-method termPrefix > ### termPrefix,Term-method termPrefix,Terms-method show,Term-method > ### show,Terms-method termId termId,Term-method termId,Terms-method > ### isObsolete isObsolete,Term-method isObsolete,Terms-method isRoot > ### isRoot,Term-method isRoot,Terms-method coerce,Term,data.frame-method > ### coerce,Terms,data.frame-method as.Term.data.frame as.Terms.data.frame > ### terms term term,Ontology,character-method > ### term,character,character-method terms,Ontology-method > ### terms,character-method children parents ancestors descendants partOf > ### derivesFrom unique,Terms-method length,Terms-method > ### lapply,Terms-method [,Terms-method [[,Terms-method > ### all.equal,Term,Term-method all.equal,Terms,Terms-method > ### Keywords: classes > > ### ** Examples > > > ## (all) terms > (gotrms <- terms("go", pagesize = 10000)) Error in curl::curl_fetch_memory(url, handle = handle) : GnuTLS recv error (-110): The TLS connection was non-properly terminated. Calls: terms ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > # 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 2.27.0 > > 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 SBO, RS ... REPR, VBO Object of class 'Ontologies' with 1 entries SBO Object of class 'Ontologies' with 2 entries SBO, RS Object of class 'Ontologies' with 3 entries SBO, RS, TGMA Object of class 'Ontologies' with 4 entries SBO, RS, TGMA, UBERON Object of class 'Ontologies' with 5 entries SBO, RS ... UBERON, TTO 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 ... hepatic immune response, glycogen catabolic process 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:0001212 Testing term SO:0000180 Testing term SO:0005849 Testing term SO:0001387 Testing term SO:0000879 Testing term SO:0001965 Testing term SO:0000932 Testing term SO:0000935 Testing term SO:0001344 Testing term SO:0000237
rols.Rcheck/rols-Ex.timings
name | user | system | elapsed | |
CVParam-class | 0.646 | 0.024 | 48.502 | |
OlsSearch-class | 0.300 | 0.091 | 24.227 | |
Ontology-class | 0.486 | 0.008 | 14.179 | |
Properties-class | 0.479 | 0.033 | 29.017 | |