############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ChIPXpress.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ChIPXpress_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPXpress.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPXpress/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPXpress’ version ‘1.46.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions 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 ‘ChIPXpress’ 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 * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘ChIPXpressData’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ChIPXpress-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ChIPXpress > ### Title: ChIPXpress Ranking > ### Aliases: ChIPXpress > ### Keywords: ChIPXpress > > ### ** Examples > > ## Example analyses of real Oct4 bound genes predicted > ## from ChIP-seq data in ESC using pre-built GPL1261 > ## database > > ## Load predicted Oct4-bound genes from ChIPx data > data(Oct4ESC_ChIPgenes) > > ## Load example GPL1261 Database > library(bigmemory) > path <- system.file("extdata",package="ChIPXpressData") > DB_GPL1261 <- attach.big.matrix("DB_GPL1261.bigmemory.desc",path=path) > ## To load the human GPL570 data, replace 'DB_GPL1261' with 'DB_GPL570'. > > ## Run ChIPXpress ("18999" is Entrez GeneID of Oct4) > out <- ChIPXpress(TFID="18999",ChIP=Oct4ESC_ChIPgenes$EntrezID,DB=DB_GPL1261) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPXpress.Rcheck/00check.log’ for details.