############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cicero.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cicero_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cicero.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'cicero/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cicero' version '1.12.1' * 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 whether package 'cicero' 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 aggregate_nearby_peaks: no visible binding for global variable 'val' annotate_cds_by_site: no visible binding for global variable 'row_name' assemble_connections : : no visible global function definition for 'patterns' assemble_connections: no visible binding for global variable 'value' estimateSizeFactorsSimp: no visible global function definition for 'sizeFactors<-' find_overlapping_ccans: no visible binding for global variable 'CCAN' generate_windows: no visible binding for global variable 'V1' plot_accessibility_in_pseudotime: no visible binding for global variable 'f_id' plot_accessibility_in_pseudotime: no visible binding for global variable 'Var1' Undefined global functions or variables: CCAN V1 Var1 f_id patterns row_name sizeFactors<- val value * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: * plotting/connections-plot-with-collapsetranscripts-true.svg * plotting/connections-plot-with-comparison-color.svg * plotting/connections-plot-with-comparison-peak-color-hex.svg * plotting/connections-plot-with-comparison-peak-color.svg * plotting/connections-plot-with-comparison.svg * plotting/connections-plot-with-gene-model-color.svg * plotting/connections-plot-with-gene-model-no-genes.svg * plotting/connections-plot-with-gene-model-with-comparison.svg * plotting/connections-plot-with-gene-model.svg * plotting/peak-color-color-column.svg * plotting/peak-color-logical-column.svg * plotting/peak-color-type-column.svg * plotting/peak-color.svg Error: Test failures Execution halted ** running tests for arch 'x64' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: * plotting/connections-plot-with-collapsetranscripts-true.svg * plotting/connections-plot-with-comparison-color.svg * plotting/connections-plot-with-comparison-peak-color-hex.svg * plotting/connections-plot-with-comparison-peak-color.svg * plotting/connections-plot-with-comparison.svg * plotting/connections-plot-with-gene-model-color.svg * plotting/connections-plot-with-gene-model-no-genes.svg * plotting/connections-plot-with-gene-model-with-comparison.svg * plotting/connections-plot-with-gene-model.svg * plotting/peak-color-color-column.svg * plotting/peak-color-logical-column.svg * plotting/peak-color-type-column.svg * plotting/peak-color.svg 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: 2 ERRORs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cicero.Rcheck/00check.log' for details.