* using log directory ‘/Users/ripley/R/packages/tests-devel/expands.Rcheck’ * using R Under development (unstable) (2021-10-05 r81008) * using platform: aarch64-apple-darwin20.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘expands/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘expands’ version ‘2.1.3’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘expands’ 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 use of S3 registration ... 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 R/sysdata.rda ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘expands-Ex.R’ failed The error most likely occurred in: > ### Name: cellfrequency_pdf > ### Title: Computes the probability distribution of cellular frequencies > ### for a single mutation. > ### Aliases: cellfrequency_pdf > > ### ** Examples > > freq=seq(0.1,1.0,by=0.01); > cfd=cellfrequency_pdf(af=0.26,cnv=1.95,pnb=0,freq=freq, max_PM=6) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : java.lang.IllegalAccessException: class RJavaTools cannot access a member of class java.util.HashMap$KeySet (in module java.base) with modifiers "public final" Calls: cellfrequency_pdf -> .map2mat -> .jrcall -> .jcall -> .jcheck Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... WARNING Error(s) in re-building vignettes: --- re-building ‘expands.Rnw’ using Sweave Error: processing vignette 'expands.Rnw' failed with diagnostics: chunk 5 Error in .local(object, ...) : object must be a numeric matrix --- failed re-building ‘expands.Rnw’ SUMMARY: processing the following file failed: ‘expands.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING See ‘/Users/ripley/R/packages/tests-devel/expands.Rcheck/00check.log’ for details. 29.37 real 26.38 user 3.39 sys