############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:G4SNVHunter.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings G4SNVHunter_1.1.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/G4SNVHunter.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘G4SNVHunter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘G4SNVHunter’ version ‘1.1.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘G4SNVHunter’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 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 files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning in checkSNV(gr1, mode = "w") : checkSNV is deprecated. Warning in checkSNV(gr3, mode = "w") : checkSNV is deprecated. Warning in plotSNVImpact(res_snp) : 'plotSNVImpact' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed G4VarImpact 318.575 2.185 320.772 plotVarImpact 102.787 1.611 104.405 plotImpactedG4 101.275 1.738 103.018 filterVarImpact 100.642 1.369 102.020 SNVImpactG4 70.130 1.456 71.591 filterSNVImpact 15.657 1.355 17.013 plotSNVImpact 15.493 1.269 16.763 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/G4SNVHunter.Rcheck/00check.log’ for details.