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###
### 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
###
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* 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols
###
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* 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)

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