##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocHail_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocHail.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.9.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocHail’ 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 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BiocHail-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_ukbb_sumstat_10kloci_mt
> ### Title: interface to a small subset of UKBB summary stats in MatrixTable
> ###   format
> ### Aliases: get_ukbb_sumstat_10kloci_mt
> 
> ### ** Examples
> 
> hl <- hail_init()
> ss <- get_ukbb_sumstat_10kloci_mt(hl)
Warning: download failed
  web resource path: ‘https://bir190004-bucket01.mghp.osn.xsede.org/BiocUKBBData/ukbb_sumst_10kloc.zip’
  local file path: ‘/home/biocbuild/.cache/R/BiocFileCache/213b5a7ae32a47_ukbb_sumst_10kloc.zip’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Transferred a partial file [bir190004-bucket01.mghp.osn.xsede.org]:
end of response with 4893741984 bytes missing
Warning: bfcadd() failed; resource removed
  rid: BFC4213
  fpath: ‘https://bir190004-bucket01.mghp.osn.xsede.org/BiocUKBBData/ukbb_sumst_10kloc.zip’
  reason: download failed
Error in .util_download(x, rid[i], proxy, progress, config, "bfcadd()",  : 
  bfcadd() failed; see warnings()
Error in fun(...) : 
  no ukbb_sumst in cache and cannot populate with download, try another method.
Calls: get_ukbb_sumstat_10kloci_mt -> <Anonymous> -> fun
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
as.data.frame                  8.181  0.989  75.568
get_1kg                        0.831  0.105   6.820
filter                         0.178  0.014   8.521
filter.hail.table.Table        0.184  0.000   6.654
as.data.frame.default          0.117  0.001   6.652
as.data.frame.hail.table.Table 0.105  0.008   5.460
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BiocHail
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BiocHail’ ...
** this is package ‘BiocHail’ version ‘1.9.4’
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocHail)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(BiocHail)

Attaching package: 'BiocHail'

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:base':

    as.data.frame

> 
> test_check("BiocHail")