* using log directory ‘/srv/hornik/tmp/CRAN/comradesOO.Rcheck’ * using R Under development (unstable) (2023-10-30 r85440) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘comradesOO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘comradesOO’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Jonathan Price ’ New submission Possibly misspelled words in DESCRIPTION: RNAs (3:55, 8:61) * 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 serialization versions ... OK * checking whether package ‘comradesOO’ can be installed ... [16s/16s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] 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 ... [21s/21s] OK * checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [16s/16s] ERROR Running examples in ‘comradesOO-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compareKnownStructures > ### Title: compareKnownStructures > ### Aliases: compareKnownStructures > ### compareKnownStructures,comradesDataSet-method > > ### ** Examples > > cds = makeExampleComradesDataSet() ******************************************** ***** COMRADES-OO ****** ******************************************** *****-------*******************-------****** ***** Reading SampleTable ****** ***** Detected 2 Samples ****** ***** detected group c:: 2 ***** ***** detected group s:: 1 ***** **** Sample Names: s1 c1 **** **** Sample Names: s1 c1 **** **** Sample Names: s1 c1 **** **** Sample Names: s1 c1 **** ***** Reading Hyb Files ***** ***** Getting RNAs of Interest ****** ***** RNA of interest + Host RNA ***** ***** RNA of interest Alone ***** ***** Making Matrices ****** ***** RNA Size: 83 ***** ***** Creating object ***** *****-------*******************-------****** ******************************************** ******************************************** > clusteredCds = clusterComrades(cds = cds, + cores = 3, + stepCount = 2, + clusterCutoff = 1) ******************************************** **** transcript1 ***** **** 83 nt **** **** Assessing Long Range **** **** Sampling Long Range **** **** Assessing Short Range **** **** Sampling short Range **** ***** done s1 1 / 1 ***** ***** done c1 1 / 1 ***** ***** Creating object ***** ******************************************** > > > trimmedClusters = trimClusters(clusteredCds = clusteredCds,trimFactor = 1, clusterCutoff = 1) ******************************************** ****** Trimming Clusters ****** ****** Saving ****** ****** Saving mat list ****** ****** Saving table list ****** ****** Saving End ****** ****** Saving mat list End ****** ****** Saving granges list ****** ****** Saving table list End ****** ******************************************** > > > > fasta = paste(c(rep('A',25), + rep('T',25), + rep('A',10), + rep('T',23)),collapse = "") > > header = '>transcript1' > > > fastaFile = tempfile() > writeLines(paste(header,fasta,sep = "\n"),con = fastaFile) > > > rnaRefs = list() > rnaRefs[[rnas(cds)]] = read.fasta(fastaFile) > rnaRefs $transcript1 $transcript1$transcript1 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" "a" [20] "a" "a" "a" "a" "a" "a" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" [39] "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "a" "a" "a" "a" "a" "a" "a" [58] "a" "a" "a" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" "t" [77] "t" "t" "t" "t" "t" "t" "t" attr(,"name") [1] "transcript1" attr(,"Annot") [1] ">transcript1" attr(,"class") [1] "SeqFastadna" > > > > foldedCds = foldComrades(trimmedClusters, + rnaRefs = rnaRefs, + start = 1, + end = 83, + shape = 0, + ensembl = 5, + constraintNumber = 1, + evCutoff = 1) sh: 2: RNAfold: not found Error in system(command, intern = T) : error in running command Calls: foldComrades -> foldComrades -> findBasePairsRNAcoFold2 -> system Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/5s] OK Running ‘testthat.R’ [4s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [43s/43s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE