############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomeInfoDb_1.42.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GenomeInfoDb.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK * this is package ‘GenomeInfoDb’ version ‘1.42.3’ * 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 ‘GenomeInfoDb’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 3.7Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed loadTaxonomyDb 8.985 0.194 9.203 GenomeDescription-class 8.867 0.220 9.120 seqlevelsStyle 4.944 0.107 26.577 getChromInfoFromNCBI 1.059 0.564 19.482 getChromInfoFromUCSC 0.852 0.036 7.078 getChromInfoFromEnsembl 0.688 0.145 103.156 NCBI-utils 0.126 0.008 16.998 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ ERROR Running the tests in ‘tests/run_unitTests.R’ failed. Last 13 lines of output: GenomeInfoDb RUnit Tests - 22 test functions, 1 error, 0 failures ERROR in test_switching_Seqinfo_between_UCSC_and_NCBI_styles: Error in download.file(url, destfile, quiet = TRUE) : download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/231/765/GCA_000231765.1_GadMor_May2010/GCA_000231765.1_GadMor_May2010_assembly_report.txt' failed Test files with failing tests test_seqlevelsStyle.R test_switching_Seqinfo_between_UCSC_and_NCBI_styles Error in BiocGenerics:::testPackage("GenomeInfoDb") : unit tests failed for package GenomeInfoDb Calls: <Anonymous> -> <Anonymous> In addition: There were 50 or more warnings (use warnings() to see the first 50) 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: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/GenomeInfoDb.Rcheck/00check.log’ for details.