############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bumphunter/DESCRIPTION’ ... OK * this is package ‘bumphunter’ version ‘1.34.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach', 'iterators', 'parallel', 'locfit' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘bumphunter’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘doParallel:::.options’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bumphunterEngine: no visible binding for global variable ‘bootstraps’ Undefined global functions or variables: bootstraps * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bumphunter 4.002 2.315 3.481 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘test-all.R’ ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: Error in `download.file(resource(con), destfile)`: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz' Backtrace: █ 1. ├─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz") test_annotation.R:99:0 2. └─BiocIO::import("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz") 3. ├─BiocIO::import(FileForFormat(con), ...) 4. └─BiocIO::import(FileForFormat(con), ...) 5. ├─BiocIO::import(con, ...) 6. └─rtracklayer::import(con, ...) 7. └─rtracklayer:::.local(con, format, text, ...) 8. └─utils::download.file(resource(con), destfile) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ] 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/bumphunter.Rcheck/00check.log’ for details.