############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CexoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CexoR_1.30.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CexoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CexoR’ version ‘1.30.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CexoR’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'CexoR' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: GPL-2 + file LICENSE * 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 ... NOTE cexor: no visible global function definition for ‘subsetByOverlaps’ Undefined global functions or variables: subsetByOverlaps * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘CexoR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CexoR-package > ### Title: An R package to uncover high-resolution protein-DNA interactions > ### in ChIP-exo replicates > ### Aliases: CexoR-package CexoR > > ### ** Examples > > > ## hg19. chr2:1-1,000,000. CTCF data from Rhee and Pugh (2011) > > owd <- setwd(tempdir()) > > rep1 <- "CTCF_rep1_chr2_1-1e6.bam" > rep2 <- "CTCF_rep2_chr2_1-1e6.bam" > rep3 <- "CTCF_rep3_chr2_1-1e6.bam" > r1 <- system.file("extdata", rep1, package="CexoR",mustWork = TRUE) > r2 <- system.file("extdata", rep2, package="CexoR",mustWork = TRUE) > r3 <- system.file("extdata", rep3, package="CexoR",mustWork = TRUE) > > chipexo <- cexor(bam=c(r1,r2,r3), chrN="chr2", chrL=1e6, idr=0.01, p=1e-18, N=3e4) Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w], : NaNs produced Error in names(x) <- value : 'names' attribute [8] must be the same length as the vector [0] Calls: cexor -> colnames<- -> colnames<- Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 1 Test Suite : CexoR RUnit Tests - 1 test function, 1 error, 0 failures ERROR in test_cexor: Error in names(x) <- value : 'names' attribute [8] must be the same length as the vector [0] Test files with failing tests test_cexor.R test_cexor Error in BiocGenerics:::testPackage("CexoR") : unit tests failed for package CexoR 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 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck/00check.log’ for details.