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NicheBarcoding

Niche-model-Based Species Identification

v1.0 · Dec 21, 2021 · GPL (>= 3)
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Description

Species Identification using DNA Barcodes Integrated with Environmental Niche Models.

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3 ERROR
3 NOTE
8 OK
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r-devel-linux-x86_64-debian-clang ERROR
r-devel-linux-x86_64-debian-gcc NOTE
r-devel-linux-x86_64-fedora-clang NOTE
r-devel-linux-x86_64-fedora-gcc NOTE
r-devel-macos-arm64 OK
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 ERROR
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 ERROR
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (15 non-OK)
NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.com>’

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.

The BugReports field in DESCRIPTION has
  https://github.com/Yangcq-Ivy/NicheBarcoding
which should likely be
  https://github.com/Yangcq-Ivy/NicheBarcoding/issues
instead.
ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.com>’

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.

The BugReports field in DESCRIPTION has
  https://github.com/Yangcq-Ivy/NicheBarcoding
which should likely be
  https://github.com/Yangcq-Ivy/NicheBarcoding/issues
instead.
NOTE r-devel-linux-x86_64-fedora-clang

dependencies in R code

Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
NOTE r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
OK r-devel-macos-arm64

*


            

            

              

                OK
                r-devel-windows-x86_64
              

              
*

              

            

            

              

                ERROR
                r-oldrel-macos-arm64
              

              
tests

              
  Running ‘testthat.R’ [25s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NicheBarcoding)
  > 
  > test_check("NicheBarcoding")
  Loading required namespace: rJava
  
   *** caught illegal operation ***
  address 0x1139eef78, cause 'illegal trap'
  
  Traceback:
   1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o",     dirout, "-s", pfn, args))
   2: .local(x, p, ...)
   3: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic")
   4: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic")
   5: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
   6: suppressWarnings(dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic"))
   7: niche.Model.Build(prese = NULL, absen = NULL, prese.env = prese.env,     absen.env = NULL, model = "MAXENT", bak.vir = bak.vir, en.vir = en.vir)
   8: NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE, model = "MAXENT",     variables = "ALL", en.vir = en.vir, bak.vir = bak.vir)
   9: eval(code, test_env)
  10: eval(code, test_env)
  11: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  15: doTryCatch(return(expr), name, parentenv, handler)
  16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  17: tryCatchList(expr, classes, parentenv, handlers)
  18: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  19: test_code(desc, code, env = parent.frame(), reporter = reporter)
  20: test_that("tests of different parameter combinations", {    data(en.vir)    data(bak.vir)    library(ape)    data(LappetMoths)    ref.seq <- LappetMoths$ref.seq    que.seq <- LappetMoths$que.seq    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE,         model = "MAXENT", variables = "ALL", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE,         model = "MAXENT", variables = "SELECT", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    ref.add <- LappetMoths$ref.add    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE,         model = "MAXENT", variables = "ALL", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE,         model = "MAXENT", variables = "SELECT", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)})
  21: eval(code, test_env)
  22: eval(code, test_env)
  23: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  27: doTryCatch(return(expr), name, parentenv, handler)
  28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  29: tryCatchList(expr, classes, parentenv, handlers)
  30: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  31: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  32: source_file(path, env = env(env), desc = desc, error_call = error_call)
  33: FUN(X[[i]], ...)
  34: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  37: tryCatchList(expr, classes, parentenv, handlers)
  38: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  39: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  40: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  41: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  42: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  43: test_check("NicheBarcoding")
  An irrecoverable exception occurred. R is aborting now ...

            

            

              

                OK
                r-oldrel-macos-x86_64
              

              
*

              

            

            

              

                OK
                r-oldrel-windows-x86_64
              

              
*

              

            

            

              

                OK
                r-patched-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-linux-x86_64
              

              
*

              

            

            

              

                ERROR
                r-release-macos-arm64
              

              
tests

              
  Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NicheBarcoding)
  > 
  > test_check("NicheBarcoding")
  Loading required namespace: rJava
  
   *** caught illegal operation ***
  address 0x10a12ef78, cause 'illegal trap'
  
  Traceback:
   1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o",     dirout, "-s", pfn, args))
   2: .local(x, p, ...)
   3: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic")
   4: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic")
   5: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
   6: suppressWarnings(dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic"))
   7: niche.Model.Build(prese = NULL, absen = NULL, prese.env = prese.env,     absen.env = NULL, model = "MAXENT", bak.vir = bak.vir, en.vir = en.vir)
   8: NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE, model = "MAXENT",     variables = "ALL", en.vir = en.vir, bak.vir = bak.vir)
   9: eval(code, test_env)
  10: eval(code, test_env)
  11: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  15: doTryCatch(return(expr), name, parentenv, handler)
  16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  17: tryCatchList(expr, classes, parentenv, handlers)
  18: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  19: test_code(desc, code, env = parent.frame(), reporter = reporter)
  20: test_that("tests of different parameter combinations", {    data(en.vir)    data(bak.vir)    library(ape)    data(LappetMoths)    ref.seq <- LappetMoths$ref.seq    que.seq <- LappetMoths$que.seq    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE,         model = "MAXENT", variables = "ALL", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE,         model = "MAXENT", variables = "SELECT", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    ref.add <- LappetMoths$ref.add    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE,         model = "MAXENT", variables = "ALL", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)    NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE,         model = "MAXENT", variables = "SELECT", en.vir = en.vir,         bak.vir = bak.vir)    expect_equal(ncol(NBSI.out), 7)})
  21: eval(code, test_env)
  22: eval(code, test_env)
  23: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  27: doTryCatch(return(expr), name, parentenv, handler)
  28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  29: tryCatchList(expr, classes, parentenv, handlers)
  30: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  31: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  32: source_file(path, env = env(env), desc = desc, error_call = error_call)
  33: FUN(X[[i]], ...)
  34: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  37: tryCatchList(expr, classes, parentenv, handlers)
  38: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  39: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  40: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  41: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  42: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  43: test_check("NicheBarcoding")
  An irrecoverable exception occurred. R is aborting now ...

            

            

              

                OK
                r-release-macos-x86_64
              

              
*

              

            

            

              

                OK
                r-release-windows-x86_64
              

              
*

              

            

          

        

      



      

      
      

        
Check History

        

          

            
              ERROR
              
                8 OK ·                 3 NOTE ·                 0 WARNING ·                 3 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  ERROR
                  r-devel-linux-x86_64-debian-clang
                

                
CRAN incoming feasibility

                
Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.com>’

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.

The BugReports field in DESCRIPTION has
  https://github.com/Yangcq-Ivy/NicheBarcoding
which should likely be
  https://github.com/Yangcq-Ivy/NicheBarcoding/issues
instead.

              

              

                

                  NOTE
                  r-devel-linux-x86_64-debian-gcc
                

                
CRAN incoming feasibility

                
Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.com>’

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.

The BugReports field in DESCRIPTION has
  https://github.com/Yangcq-Ivy/NicheBarcoding
which should likely be
  https://github.com/Yangcq-Ivy/NicheBarcoding/issues
instead.

              

              

                

                  NOTE
                  r-devel-linux-x86_64-fedora-clang
                

                
dependencies in R code

                
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.

              

              

                

                  NOTE
                  r-devel-linux-x86_64-fedora-gcc
                

                
dependencies in R code

                
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.

              

              

                

                  ERROR
                  r-release-macos-arm64
                

                
tests

                
  Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NicheBarcoding)
  > 
  > test_check("NicheBarcoding")
  Loading required namespace: rJava
  
   *** caught illegal operation ***
  address 0x10a12ef78, cause 'illegal trap'
  
  Traceback:
   1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o",     dirout, "-s", pfn, args))
   2: .local(x, p, ...)
   3: dismo::maxent(Data[, -1], Data[, 1], args = "outputf

              

              

                

                  ERROR
                  r-oldrel-macos-arm64
                

                
tests

                
  Running ‘testthat.R’ [25s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NicheBarcoding)
  > 
  > test_check("NicheBarcoding")
  Loading required namespace: rJava
  
   *** caught illegal operation ***
  address 0x1139eef78, cause 'illegal trap'
  
  Traceback:
   1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o",     dirout, "-s", pfn, args))
   2: .local(x, p, ...)
   3: dismo::maxent(Data[, -1], Data[, 1], args = "outputf

              

            

          

        

      


      

      
      

        
Dependency Network

        

          
            

            
            
            Dependencies
            
            Reverse dependencies

            
            
            
            
            
            
            
            
            
            
            

            

            
            
              
              ape
            
            
              
              dismo
            
            
              
              e1071
            
            
              
              maps
            
            
              
              pROC
            
            
              
              randomForest
            
            
              
              raster
            
            
              
              rJava
            
            
              
              spider
            
            
              
              vegan
            

            

            
            
            NicheBarcoding
          
        

      


      
      

        
Version History

        

          

            new
            1.0
            Mar 9, 2026