##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HumanTranscriptomeCompendium.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HumanTranscriptomeCompendium_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/HumanTranscriptomeCompendium.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HumanTranscriptomeCompendium/DESCRIPTION’ ... OK
* this is package ‘HumanTranscriptomeCompendium’ version ‘1.20.0’
* 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 ‘HumanTranscriptomeCompendium’ 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 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘HumanTranscriptomeCompendium-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: htx_query_by_study_accession
> ### Title: retrieve 'restfulSE' SummarizedExperiment instance for selected
> ###   studies in htx compendium
> ### Aliases: htx_query_by_study_accession
> 
> ### ** Examples
> 
> htx_query_by_study_accession("ERP011411")
acquiring base restfulSE...
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [bcfound-bigrna.s3.amazonaws.com] SSL connection timeout
Calls: htx_query_by_study_accession ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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:
    3.     ├─BiocFileCache::bfcneedsupdate(cache, qans$rid[1])
    4.     └─BiocFileCache::bfcneedsupdate(cache, qans$rid[1])
    5.       └─base::vapply(rids, helper, logical(1), x = x)
    6.         └─BiocFileCache (local) FUN(X[[i]], ...)
    7.           └─BiocFileCache:::.httr_get_cache_info(fpath)
    8.             ├─base::withCallingHandlers(...)
    9.             └─httr::HEAD(link)
   10.               └─httr:::request_perform(req, hu$handle$handle)
   11.                 ├─httr:::request_fetch(req$output, req$url, handle)
   12.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   13.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/HumanTranscriptomeCompendium.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HumanTranscriptomeCompendium
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘HumanTranscriptomeCompendium’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 'HumanTranscriptomeCompendium' is deprecated and will be
  removed from Bioconductor version 3.20. Please see rhdf5client as
  replacement.
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HumanTranscriptomeCompendium' is deprecated and will be
  removed from Bioconductor version 3.20. Please see rhdf5client as
  replacement.
** testing if installed package keeps a record of temporary installation path
* DONE (HumanTranscriptomeCompendium)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(HumanTranscriptomeCompendium)
Warning message:
In fun(libname, pkgname) :
  Package 'HumanTranscriptomeCompendium' is deprecated and will be
  removed from Bioconductor version 3.20. Please see rhdf5client as
  replacement.
> 
> test_check("HumanTranscriptomeCompendium")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_htc.R:23:1'): (code run outside of `test_that()`) ──────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [bcfound-bigrna.s3.amazonaws.com] SSL connection timeout
Backtrace:
     ▆
  1. └─HumanTranscriptomeCompendium::htx_load() at test_htc.R:23:1
  2.   └─HumanTranscriptomeCompendium:::htx_check_cache(cache)
  3.     ├─BiocFileCache::bfcneedsupdate(cache, qans$rid[1])
  4.     └─BiocFileCache::bfcneedsupdate(cache, qans$rid[1])
  5.       └─base::vapply(rids, helper, logical(1), x = x)
  6.         └─BiocFileCache (local) FUN(X[[i]], ...)
  7.           └─BiocFileCache:::.httr_get_cache_info(fpath)
  8.             ├─base::withCallingHandlers(...)
  9.             └─httr::HEAD(link)
 10.               └─httr:::request_perform(req, hu$handle$handle)
 11.                 ├─httr:::request_fetch(req$output, req$url, handle)
 12.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 13.                   └─curl::curl_fetch_memory(url, handle = handle)

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