############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENCODExplorer_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ENCODExplorer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ENCODExplorer' version '2.18.0' * 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 whether package 'ENCODExplorer' 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE createDesign: no visible binding for global variable 'file_format' createDesign: no visible binding for global variable 'status' createDesign: no visible binding for global variable 'accession' createDesign: no visible binding for global variable 'controls' createDesign : get_ctrl_design: no visible binding for global variable 'accession' createDesign : get_ctrl_design: no visible binding for global variable 'href' createDesign: no visible global function definition for '.' createDesign: no visible binding for global variable 'href' createDesign: no visible binding for global variable 'Experiment' createDesign: no visible binding for global variable 'Value' downloadEncode: no visible binding for global variable 'file_accession' downloadEncode: no visible binding for global variable 'file_format' downloadEncode: no visible binding for global variable 'accession' shinyEncode: no visible binding for global variable 'ui' shinyEncode: no visible binding for global variable 'server' Undefined global functions or variables: . Experiment Value accession controls file_accession file_format href server status ui * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_encode_df_full 58.46 8.48 68.24 ENCODEBindingConsensus-class 33.11 1.92 40.42 queryTranscriptExpression 5.32 1.81 15.72 buildExpressionSummary 6.12 0.14 19.06 ENCODEExpressionSummary-class 4.49 1.05 12.28 buildConsensusPeaks 2.28 0.25 17.84 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_encode_df_full 50.28 0.84 51.82 ENCODEBindingConsensus-class 29.64 0.66 37.38 queryTranscriptExpression 5.03 0.41 15.00 buildExpressionSummary 5.12 0.22 18.50 queryConsensusPeaks 5.16 0.01 5.18 ENCODEExpressionSummary-class 3.80 0.42 12.08 buildConsensusPeaks 2.43 0.08 14.58 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' ERROR Running the tests in 'tests/runTests.R' failed. Last 13 lines of output: 1 Test Suite : ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : Test not TRUE res should be get an accession entry Test files with failing tests test_search.R test.ret_content Error in BiocGenerics:::testPackage("ENCODExplorer") : unit tests failed for package ENCODExplorer Execution halted ** running tests for arch 'x64' ... Running 'runTests.R' ERROR Running the tests in 'tests/runTests.R' failed. Last 13 lines of output: 1 Test Suite : ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : Test not TRUE res should be get an accession entry Test files with failing tests test_search.R test.ret_content Error in BiocGenerics:::testPackage("ENCODExplorer") : unit tests failed for package ENCODExplorer 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: 2 ERRORs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/00check.log' for details.