• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 19.1.3     flang-new version 19.1.3
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘orthGS/DESCRIPTION’ ... OK
• this is package ‘orthGS’ version ‘0.1.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘muscle’
• 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 ‘orthGS’ can be installed ... [21s/30s] OK See the install log for details.
• 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 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 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 ... [29s/30s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [12s/12s] ERROR Running examples in ‘orthGS-Ex.R’ failed The error most likely occurred in: > ### Name: gapless_msa > ### Title: Remove Gaps in a MSA > ### Aliases: gapless_msa > > ### ** Examples > > gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),ids = c("a", "b", "c"))$ali) Error in msa(sequences = c("APGW", "AGWC", "CWGA"), ids = c("a", "b", :   You must install the package muscle in order to use this function Calls: gapless_msa -> as.matrix -> msa Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/24s] ERROR Error(s) in re-building vignettes: --- re-building ‘Searching_for_Orthologous.Rmd’ using rmarkdown Quitting from lines 56-61 [unnamed-chunk-5] (Searching_for_Orthologous.Rmd) Error: processing vignette 'Searching_for_Orthologous.Rmd' failed with diagnostics: You must install the package muscle in order to use this function --- failed re-building ‘Searching_for_Orthologous.Rmd’ --- re-building ‘Unraveling_the_hiden_paralogous.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/orthGS.Rcheck/vign_test/orthGS/vignettes/Unraveling_the_hiden_paralogous_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19334 bytes Input file size = 19436 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15210   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15210 Output IDAT size = 15210 bytes (4124 bytes decrease) Output file size = 15288 bytes (4148 bytes = 21.34% decrease) --- finished re-building ‘Unraveling_the_hiden_paralogous.Rmd’ SUMMARY: processing the following file failed:   ‘Searching_for_Orthologous.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs