############################################################################## ############################################################################## ### ### 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_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocHail.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 ‘1.6.1’ * 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_1kg > ### Title: interface to 1kg import > ### Aliases: get_1kg > > ### ** Examples > > hl <- hail_init() > mt <- get_1kg(hl) Warning: download failed web resource path: ‘https://bir190004-bucket01.mghp.osn.xsede.org/BiocHailData/1kg.zip’ local file path: ‘/home/biocbuild/.cache/R/BiocFileCache/1d48d75123948c_1kg.zip’ reason: Transferred a partial file [bir190004-bucket01.mghp.osn.xsede.org]: transfer closed with 8114584 bytes remaining to read Warning: bfcadd() failed; resource removed rid: BFC3237 fpath: ‘https://bir190004-bucket01.mghp.osn.xsede.org/BiocHailData/1kg.zip’ reason: download failed Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : bfcadd() failed; see warnings() Error in fun(...) : no hail_tut_mt in cache and cannot populate with download, try another method. Calls: get_1kg -> -> fun Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’