############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromstaR_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/chromstaR.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chromstaR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chromstaR’ version ‘1.29.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘chromstaR’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 4.5Mb * 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 whether startup messages can be suppressed ... 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 Chromstar: multiple local function definitions for ‘parallel.helper’ with different formal arguments * checking Rd files ... NOTE checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces 66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces 66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces 60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces 60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) plotGenomeBrowser.Rd:28-68: Lost braces 28 | plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol='black', peakcols=NULL, style='peaks', peakTrackHeight=5) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:36-41: Lost braces 36 | if (style == 'peaks') { | ^ checkRd: (-1) plotGenomeBrowser.Rd:41-45: Lost braces 41 | } else if (style == 'density') { | ^ checkRd: (-1) plotGenomeBrowser.Rd:45-47: Lost braces 45 | } else { | ^ checkRd: (-1) plotGenomeBrowser.Rd:50-65: Lost braces 50 | if (!is.null(peaklist)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:51-53: Lost braces 51 | if (is.null(peakcols)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:54-64: Lost braces 54 | for (i1 in 1:length(peaklist)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:57-60: Lost braces 57 | if (length(peaks) > 0) { | ^ * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘chromstaR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotExpression > ### Title: Overlap with expression data > ### Aliases: plotExpression > > ### ** Examples > > ## Load an example multiHMM > file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData", + package="chromstaR") > model <- get(load(file)) > > ## Obtain expression data > data(expression_lv) > head(expression_lv) ensembl_gene_id expression_BN expression_SHR 1 ENSRNOG00000000001 8.8 7.4 2 ENSRNOG00000000007 20.0 13.0 3 ENSRNOG00000000008 1.8 3.4 4 ENSRNOG00000000010 6.2 506.8 5 ENSRNOG00000000012 48.0 36.4 6 ENSRNOG00000000014 18.2 15.2 > > ## We need to get coordinates for each of the genes > library(biomaRt) > ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') Ensembl site unresponsive, trying useast mirror Ensembl site unresponsive, trying asia mirror Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : Unable to query any Ensembl site Calls: useEnsembl -> .chooseEnsemblMirror Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/chromstaR.Rcheck/00check.log’ for details.