* using log directory ‘/srv/hornik/tmp/CRAN_pretest/NicheBarcoding.Rcheck’ * using R Under development (unstable) (2024-08-29 r87078) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘NicheBarcoding/DESCRIPTION’ ... OK * this is package ‘NicheBarcoding’ version ‘0.0.1.8000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] WARNING Maintainer: ‘Cai-qing Yang ’ Insufficient package version (submitted: 0.0.1.8000, existing: 1.0) Version contains large components (0.0.1.8000) New maintainer: Cai-qing Yang Old maintainer(s): Cai-qing YANG Possibly misspelled words in DESCRIPTION: barcodes (7:47) Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. DESCRIPTION fields with placeholder content: Title: what the package does (one line, title case) Size of tarball: 10858424 bytes * 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 ‘NicheBarcoding’ can be installed ... [1s/1s] WARNING Found the following significant warnings: Note: break used in wrong context: no loop is visible See ‘/srv/hornik/tmp/CRAN_pretest/NicheBarcoding.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘LICENSE.md’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘car’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] 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 ... WARNING Variables with usage in Rd file 'LappetMoths.Rd' but not in code: ‘LappetMoths’ Variables with usage in Rd file 'bak.vir.Rd' but not in code: ‘bak.vir’ Variables with usage in Rd file 'en.vir.Rd' but not in code: ‘en.vir’ * 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 ... [6s/6s] OK * checking data for ASCII and uncompressed saves ... WARNING Warning: package needs dependence on R (>= 2.10) * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘NBSI.Rmd’ ‘how-to-do-stuff-NBSI.Rmd’ ‘how_it_works.Rmd’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... [7s/7s] ERROR Running examples in ‘NicheBarcoding-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: NBSI > ### Title: Niche-model-Based Species Identification (NBSI) > ### Aliases: NBSI > ### Keywords: NBSI > > ### ** Examples > > data(en.vir) > data(bak.vir) > #envir<-raster::getData("worldclim",download=FALSE,var="bio",res=2.5) > #en.vir<-raster::brick(envir) > #back<-dismo::randomPoints(mask=en.vir,n=5000,ext=NULL,extf=1.1, > # excludep=TRUE,prob=FALSE, > # cellnumbers=FALSE,tryf=3,warn=2, > # lonlatCorrection=TRUE) > #bak.vir<-raster::extract(en.vir,back) > > library(ape) > data(LappetMoths) > ref.seq<-LappetMoths$ref.seq[1:50,] > que.seq<-LappetMoths$que.seq[1:5,] > NBSI.out<-NBSI(ref.seq,que.seq,ref.add=NULL, + model="RF",en.vir=en.vir,bak.vir=bak.vir) Error in loadNamespace(x) : there is no package called ‘car’ Calls: NBSI ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in ‘tests’ ... WARNING 'library' or 'require' call not declared from: ‘testthat’ * checking tests ... [0s/0s] ERROR Running ‘testthat.R’ [0s/0s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) Error in library(testthat) : there is no package called 'testthat' Execution halted * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 7 WARNINGs, 2 NOTEs