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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RLHub.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RLHub_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/RLHub.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘RLHub/DESCRIPTION’ ... OK
* this is package ‘RLHub’ version ‘1.10.0’
* 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 ‘RLHub’ 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 code 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 loading without being on the library search path ... OK
* checking whether 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 ... NOTE
Package unavailable to check Rd xrefs: ‘Boruta’
* 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 ‘RLHub-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gene_exp
> ### Title: Gene Expression
> ### Aliases: gene_exp
> 
> ### ** Examples
> 
> 
> geneExp <- gene_exp()
see ?RLHub and browseVignettes('RLHub') for documentation
loading from cache
require(“SummarizedExperiment”)
Error: failed to load resource
  name: EH6798
  title: Gene Expression
  reason: require(“SummarizedExperiment”) failed: use BiocManager::install() to install package?
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:
   10.         └─ExperimentHub (local) .local(x, i, j = j, ...)
   11.           ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
   12.           │ └─base::eval(call, callEnv)
   13.           │   └─base::eval(call, callEnv)
   14.           └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
   15.             └─AnnotationHub (local) .local(x, i, j = j, ...)
   16.               └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   17.                 └─base::tryCatch(...)
   18.                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   19.                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   20.                       └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/RLHub.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RLHub
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RLHub’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'RLHub' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'RLHub' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (RLHub)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> library(testthat)
> library(RLHub)
Warning message:
In fun(libname, pkgname) :
  Package 'RLHub' is deprecated and will be removed from Bioconductor
  version 3.20
> 
> test_check("RLHub")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-RLHub.R:14:13'): Test accessors in RLHub ───────────────────────
Error: failed to load resource
  name: EH6798
  title: Gene Expression
  reason: require("SummarizedExperiment") failed: use BiocManager::install() to install package?
Backtrace:
     ▆
  1. └─base::lapply(...) at test-RLHub.R:9:5
  2.   └─RLHub (local) FUN(X[[i]], ...)
  3.     ├─testthat::expect_true(cls %in% class(fxn())) at test-RLHub.R:14:13
  4.     │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  5.     │   └─rlang::eval_bare(expr, quo_get_env(quo))
  6.     ├─cls %in% class(fxn())
  7.     └─RLHub (local) fxn()
  8.       ├─eh[[ehid, verbose = !quiet]]
  9.       └─eh[[ehid, verbose = !quiet]]
 10.         └─ExperimentHub (local) .local(x, i, j = j, ...)
 11.           ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
 12.           │ └─base::eval(call, callEnv)
 13.           │   └─base::eval(call, callEnv)
 14.           └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
 15.             └─AnnotationHub (local) .local(x, i, j = j, ...)
 16.               └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 17.                 └─base::tryCatch(...)
 18.                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 19.                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20.                       └─value[[3L]](cond)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
Error: Test failures
Execution halted