############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:immunotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings immunotation_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘immunotation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘immunotation’ version ‘1.4.0’ * 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 ‘immunotation’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 3.9Mb extdata 2.2Mb * 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 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_allele_frequency 3.919 0.303 8.235 query_haplotype_frequencies 0.937 0.103 7.461 * 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: encode_MAC("foo") not equal to "A service failures was logged. Contact administrator for more information". 1/1 mismatches x[1]: "No Locus for allele: foo" y[1]: "A service failures was logged. Contact administrator for more informatio y[1]: n" [ FAIL 1 | WARN 0 | SKIP 0 | PASS 145 ] Error: Test failures In addition: Warning messages: 1: closing unused connection 9 (https://iamnotanurl) 2: closing unused connection 8 (https://iamnotanurl) 3: closing unused connection 6 (https://iamnotanurl) 4: closing unused connection 5 (https://iamnotanurl) 5: closing unused connection 4 (https://iamnotanurl) 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck/00check.log’ for details.