CHECK report for rols on celaya2
This page was generated on 2020-01-16 13:35:00 -0500 (Thu, 16 Jan 2020).
rols 2.15.0
Laurent Gatto
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/rols |
| Branch: master |
| Last Commit: 5ba2d38 |
| Last Changed Date: 2019-10-29 13:36:12 -0500 (Tue, 29 Oct 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rols_2.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rols.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.15.0’
* 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 cx[["_embedded"]] : subscript out of bounds
Calls: terms -> terms -> .terms -> append -> lapply
Execution halted
* 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:
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 75 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 10 ]
1. Error: CVParam creation and coercion 2 (@test_CVParam.R#34)
2. Error: Convert char to CVParam (@test_CVParam.R#50)
3. Error: OlsSearch tgn (@test_OlsSearch.R#15)
4. Error: OlsSearch ESI (@test_OlsSearch.R#30)
5. Error: OlsSearch coercion (@test_OlsSearch.R#74)
6. Error: Ontology accessors (@test_Onologies.R#63)
7. Error: Property constructors (@test_Properties.R#4)
8. Error: Property/ies show (@test_Properties.R#46)
9. Error: iterating over next property (@test_Properties.R#55)
10. Error: (unknown) (@test_Terms.R#4)
Error: testthat unit tests failed
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: 2 ERRORs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/rols.Rcheck/00check.log’
for details.
Installation output
rols.Rcheck/00install.out
Tests output
rols.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 2.15.0
>
> test_check("rols")
[, , Hello, World]
── 1. Error: CVParam creation and coercion 2 (@test_CVParam.R#34) ─────────────
Internal Server Error (HTTP 500).
Backtrace:
1. rols::CVParam(label = "MS", name = cv@name)
2. methods::new("CVParam", label = label, name = name, accession = accession)
4. Biobase::initialize(value, ...)
5. Biobase:::.local(.Object, ...)
9. methods:::.nextMethod(.Object, ...)
10. methods::validObject(.Object)
13. rols:::validityMethod(object)
15. rols::term(object@label, object@accession)
16. rols:::.term(object, id, ...)
17. httr::stop_for_status(x)
── 2. Error: Convert char to CVParam (@test_CVParam.R#50) ─────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. methods::as(x, "CVParam")
2. rols:::asMethod(object)
4. base::lapply(from, cvCharToCVPar)
5. rols:::FUN(X[[i]], ...)
6. rols::CVParam(label = from[1], accession = from[2])
9. rols::term(label, accession)
10. rols:::.term(object, id, ...)
11. httr::stop_for_status(x)
── 3. Error: OlsSearch tgn (@test_OlsSearch.R#15) ─────────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. testthat::expect_identical(...)
6. methods::as(tgn, "Terms")
7. rols:::asMethod(object)
8. base::apply(...)
9. rols:::FUN(newX[, i], ...)
11. rols::term(x[["ontology_prefix"]], x[["obo_id"]])
12. rols:::.term(object, id, ...)
13. httr::stop_for_status(x)
── 4. Error: OlsSearch ESI (@test_OlsSearch.R#30) ─────────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. testthat::expect_true(...)
6. methods::as(esi1, "Terms")
7. rols:::asMethod(object)
8. base::apply(...)
9. rols:::FUN(newX[, i], ...)
11. rols::term(x[["ontology_prefix"]], x[["obo_id"]])
12. rols:::.term(object, id, ...)
13. httr::stop_for_status(x)
Object of class 'OlsSearch':
ontolgy: GO
query: cell
requested: 20 (out of 10012)
response(s): 0
── 5. Error: OlsSearch coercion (@test_OlsSearch.R#74) ────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. methods::as(res, "Terms")
2. rols:::asMethod(object)
3. base::apply(...)
4. rols:::FUN(newX[, i], ...)
6. rols::term(x[["ontology_prefix"]], x[["obo_id"]])
7. rols:::.term(object, id, ...)
8. httr::stop_for_status(x)
Object of class 'Ontologies' with 243 entries
AERO, AFO ... ZECO, ZFS
Object of class 'Ontologies' with 1 entries
AERO
Object of class 'Ontologies' with 2 entries
AERO, AFO
Object of class 'Ontologies' with 3 entries
AERO, AFO, AGRO
Object of class 'Ontologies' with 4 entries
AERO, AFO, AGRO, APO
Object of class 'Ontologies' with 5 entries
AERO, AFO ... APO, APOLLO_SV
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2020-01-06 Updated: 2020-01-16 Version: 2020-01-01
50119 terms 61 properties 0 individuals
── 6. Error: Ontology accessors (@test_Onologies.R#63) ────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. rols::olsRoot(ol["go"])
2. rols::olsRoot(ol["go"])
3. rols:::.local(object, ...)
5. base::lapply(object@x, olsRoot)
7. rols:::FUN(X[[i]], ...)
8. rols:::.local(object, ...)
10. rols::olsRoot(olsPrefix(object))
11. rols:::.local(object, ...)
12. httr::stop_for_status(x)
── 7. Error: Property constructors (@test_Properties.R#4) ─────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. rols::properties("so")
2. rols::properties("so")
3. rols:::.properties(object, ...)
4. rols:::makeProperties(url)
5. httr::stop_for_status(x)
── 8. Error: Property/ies show (@test_Properties.R#46) ────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. testthat::expect_null(show(properties("so")))
6. rols::properties("so")
7. rols:::.properties(object, ...)
8. rols:::makeProperties(url)
9. httr::stop_for_status(x)
── 9. Error: iterating over next property (@test_Properties.R#55) ─────────────
Internal Server Error (HTTP 500).
Backtrace:
1. rols::properties(go)
2. rols::properties(go)
3. rols:::.properties(olsNamespace(object), ...)
4. rols:::makeProperties(url)
5. httr::stop_for_status(x)
── 10. Error: (unknown) (@test_Terms.R#4) ─────────────────────────────────────
Internal Server Error (HTTP 500).
Backtrace:
1. rols::term(go, "GO:0032801")
2. rols::term(go, "GO:0032801")
3. rols:::.term(object, id, ...)
4. httr::stop_for_status(x)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 75 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 10 ]
1. Error: CVParam creation and coercion 2 (@test_CVParam.R#34)
2. Error: Convert char to CVParam (@test_CVParam.R#50)
3. Error: OlsSearch tgn (@test_OlsSearch.R#15)
4. Error: OlsSearch ESI (@test_OlsSearch.R#30)
5. Error: OlsSearch coercion (@test_OlsSearch.R#74)
6. Error: Ontology accessors (@test_Onologies.R#63)
7. Error: Property constructors (@test_Properties.R#4)
8. Error: Property/ies show (@test_Properties.R#46)
9. Error: iterating over next property (@test_Properties.R#55)
10. Error: (unknown) (@test_Terms.R#4)
Error: testthat unit tests failed
Execution halted
Example timings
rols.Rcheck/rols-Ex.timings