############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BaalChIP_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BaalChIP.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 ‘BaalChIP/DESCRIPTION’ ... OK * this is package ‘BaalChIP’ version ‘1.28.0’ * 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 ‘BaalChIP’ can be installed ... OK * checking installed package size ... NOTE installed size is 196.7Mb sub-directories of 1Mb or more: data 94.2Mb test 101.9Mb * 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 ... OK * 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 LazyData ... WARNING LazyData DB of 94.2 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BaalChIP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: BaalChIP.run > ### Title: Method BaalChIP.run > ### Aliases: BaalChIP.run BaalChIP.run,BaalChIP-method > > ### ** Examples > > samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP") > hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"), + "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP")) > res <- BaalChIP(samplesheet=samplesheet, hets=hets) -samplesheet checks: OK! > res <- BaalChIP.run(res, cores=2) -computing allele counts per BAM | | | 0% | |==== | 6% | |========= | 12% | |============= | 19% | |================== | 25% | |====================== | 31% | |========================== | 38% | |=============================== | 44% | |=================================== | 50% | |======================================= | 56% | |============================================ | 62% | |================================================ | 69% | |==================================================== | 75% | |========================================================= | 81% | |============================================================= | 88% | |================================================================== | 94% | |======================================================================| 100% -applying filters per BAM | | | 0% | |==== | 6% | |========= | 12% | |============= | 19% | |================== | 25% | |====================== | 31% | |========================== | 38% | |=============================== | 44% | |=================================== | 50% | |======================================= | 56% | |============================================ | 62% | |================================================ | 69% | |==================================================== | 75% | |========================================================= | 81% | |============================================================= | 88% | |================================================================== | 94% | |======================================================================| 100% -merging replicated samples... -filtering out SNPs with only 1 observed allele... -QC complete! -geting ASB counts... will use RAF values for MCF7 group from hets file will use RAF values for GM12891 group from hets file ... calculating ASB for: MCF7 * 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, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/BaalChIP.Rcheck/00check.log’ for details.