############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings biodbMirbase_1.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbMirbase.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘biodbMirbase/DESCRIPTION’ ... OK * this is package ‘biodbMirbase’ version ‘1.5.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbMirbase’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 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 for missing documentation entries ... WARNING Undocumented code objects: ‘MirbaseMatureConn’ ‘MirbaseMatureEntry’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... NONE * 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: method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) ``(conn = ``) 3. └─conn$getEntryIds(max.results = max) 4. └─private$doGetEntryIds(max.results = max.results, ...) 5. └─self$download() 6. └─private$doDownload() 7. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 8. └─utils::download.file(...) [ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ] 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 ... ‘biodbMirbase.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘biodbMirbase.Rmd’ using rmarkdown trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Quitting from lines 65-67 [unnamed-chunk-4] (biodbMirbase.Rmd) Error: processing vignette 'biodbMirbase.Rmd' failed with diagnostics: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' --- failed re-building ‘biodbMirbase.Rmd’ SUMMARY: processing the following file failed: ‘biodbMirbase.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING See ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbMirbase.Rcheck/00check.log’ for details.