Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 1755/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rols 2.28.0 (landing page) Laurent Gatto
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the rols package: - 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: rols |
Version: 2.28.0 |
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_2.28.0.tar.gz |
StartedAt: 2023-10-18 20:17:20 -0400 (Wed, 18 Oct 2023) |
EndedAt: 2023-10-18 20:32:41 -0400 (Wed, 18 Oct 2023) |
EllapsedTime: 921.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: rols.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rols.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘2.28.0’ * 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 startup messages can be suppressed ... 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 65.156 1.796 429.229 CVParam-class 0.499 0.090 16.860 Properties-class 0.373 0.016 5.902 Ontology-class 0.364 0.017 5.198 OlsSearch-class 0.222 0.019 8.432 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Failure ('test_Onologies.R:89:5'): Ontology accessors ─────────────────────── olsTitle(go) not identical to "Gene Ontology". target is NULL, current is character ── Failure ('test_Onologies.R:91:5'): Ontology accessors ─────────────────────── olsDesc(go) not identical to "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.". target is NULL, current is character ── Failure ('test_Onologies.R:133:5'): all.equal ontolgies ───────────────────── all.equal(ol, ol0) not equal to paste0("Ontology '", nm, "': loaded: 1 string mismatch"). 1/1 mismatches x[1]: "Ontology 'aism': loaded: target is NULL, current is character" y[1]: "Ontology 'aism': loaded: 1 string mismatch" [ FAIL 4 | WARN 0 | SKIP 1 | PASS 190 ] Error: Test failures Execution halted * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rols.Rcheck/00check.log’ for details.
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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 2.28.0 > > 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 244 entries AISM, AMPHX ... CPONT, CCF Object of class 'Ontologies' with 1 entries AISM Object of class 'Ontologies' with 2 entries AISM, AMPHX Object of class 'Ontologies' with 3 entries AISM, AMPHX, ADO Object of class 'Ontologies' with 4 entries AISM, AMPHX, ADO, APO Object of class 'Ontologies' with 5 entries AISM, AMPHX ... APO, AGRO Ontology: (go) Loaded: Updated: 2023-10-09 Version: 0 terms 0 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 ... Vertebrata <vertebrates>, hepatobiliary system 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:0001756 Testing term SO:0001398 Testing term SO:0000658 Testing term SO:0001072 Testing term SO:0001424 Testing term SO:0001294 Testing term SO:0000041 Testing term SO:0000703 Testing term SO:0000876 Testing term SO:0001382 [ FAIL 4 | WARN 0 | SKIP 1 | PASS 190 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_CVParam.R:31:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_Onologies.R:49:5'): Ontology accessors ─────────────────────── ymd(olsLoaded(go)) not identical to loaded[i]. Numeric: lengths (0, 1) differ ── Failure ('test_Onologies.R:89:5'): Ontology accessors ─────────────────────── olsTitle(go) not identical to "Gene Ontology". target is NULL, current is character ── Failure ('test_Onologies.R:91:5'): Ontology accessors ─────────────────────── olsDesc(go) not identical to "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.". target is NULL, current is character ── Failure ('test_Onologies.R:133:5'): all.equal ontolgies ───────────────────── all.equal(ol, ol0) not equal to paste0("Ontology '", nm, "': loaded: 1 string mismatch"). 1/1 mismatches x[1]: "Ontology 'aism': loaded: target is NULL, current is character" y[1]: "Ontology 'aism': loaded: 1 string mismatch" [ FAIL 4 | WARN 0 | SKIP 1 | PASS 190 ] Error: Test failures Execution halted
rols.Rcheck/rols-Ex.timings
name | user | system | elapsed | |
CVParam-class | 0.499 | 0.090 | 16.860 | |
OlsSearch-class | 0.222 | 0.019 | 8.432 | |
Ontology-class | 0.364 | 0.017 | 5.198 | |
Properties-class | 0.373 | 0.016 | 5.902 | |
Term-class | 65.156 | 1.796 | 429.229 | |