• using R Under development (unstable) (2025-09-11 r88811)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.0     flang version 21.1.0
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘assignPOP/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘assignPOP’ version ‘1.3.0’
• package encoding: UTF-8
• 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 ‘assignPOP’ can be installed ... [37s/48s] OK See the install log for details.
• checking installed package size ... OK
• checking package 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 ... [7s/10s] 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 ... [64s/80s] 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 examples ... [10s/13s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [13s/15s] ERROR   Running ‘testthat.R’ [12s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(assignPOP)   >   > test_check("assignPOP")        Correct assignment rates were estimated!!     A total of 3 assignment tests for 3 pops.     Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.     Correct assignment rates were estimated!!     A total of 3 assignment tests for 3 pops.     Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.     Converting data format...        Encoding genetic data...        ################ assignPOP v1.3.0 ################        A GENEPOP format file was successfully imported!        Imported Data Info: 24 obs. by 5 loci (diploid)     Number of pop: 3     Number of inds (pop.1): 8     Number of inds (pop.2): 10     Number of inds (pop.3): 6     DataMatrix: 24 rows by 20 columns, with 19 allele variables        Data output in a list comprising the following three elements:     YOUR_LIST_NAME$DataMatrix     YOUR_LIST_NAME$SampleID     YOUR_LIST_NAME$LocusName           Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     3 assignment tests completed!!     Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     3 assignment tests completed!!     Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     6 assignment tests completed!!     Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     12 assignment tests completed!!     Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     12 assignment tests completed!!     Parallele computing is off. Analyzing data using 1 CPU core...        Monte-Carlo cross-validation done!!     3 assignment tests completed!!     Converting data format...        Encoding genetic data...        ################ assignPOP v1.3.0 ################        A GENEPOP format file was successfully imported!        Imported Data Info: 24 obs. by 5 loci (diploid)     Number of pop: 3     Number of inds (pop.1): 8     Number of inds (pop.2): 10     Number of inds (pop.3): 6     DataMatrix: 24 rows by 20 columns, with 19 allele variables        Data output in a list comprising the following three elements:     YOUR_LIST_NAME$DataMatrix     YOUR_LIST_NAME$SampleID     YOUR_LIST_NAME$LocusName           Converting data format...        Encoding genetic data...        ################ assignPOP v1.3.0 ################        A GENEPOP format file was successfully imported!        Imported Data Info: 24 obs. by 5 loci (diploid)     Number of pop: 1     Number of inds (pop.1): 24     DataMatrix: 24 rows by 20 columns, with 19 allele variables        Data output in a list comprising the following three elements:     YOUR_LIST_NAME$DataMatrix     YOUR_LIST_NAME$SampleID     YOUR_LIST_NAME$LocusName           Known and unknown datasets have identical features.     Performing PCA on genetic data for dimensionality reduction...     Assignment test is done! See results in your designated folder.     Predicted populations and probabilities are saved in [AssignmentResult.txt]     Converting data format...        Encoding genetic data...        ################ assignPOP v1.3.0 ################        A GENEPOP format file was successfully imported!        Imported Data Info: 24 obs. by 5 loci (diploid)     Number of pop: 3     Number of inds (pop.1): 8     Number of inds (pop.2): 10     Number of inds (pop.3): 6     DataMatrix: 24 rows by 20 columns, with 19 allele variables        Data output in a list comprising the following three elements:     YOUR_LIST_NAME$DataMatrix     YOUR_LIST_NAME$SampleID     YOUR_LIST_NAME$LocusName           Parallele computing is off. Analyzing data using 1 CPU core...        K-fold cross-validation done!!     3 assignment tests completed!! Import a .CSV file.     4 additional variables detected.     Checking variable data type...      ng1(integer) ng2(integer) ng3(integer) ng4(integer)     New data set created!!     It has 24 observations by 24 variables     including 4 loci(19 alleles) plus 4 additional variables(4 columns)     Parallele computing is off. Analyzing data using 1 CPU core...        K-fold cross-validation done!!     3 assignment tests completed!!     Convert population label to factor.     ng1(integer) ng2(integer) ng3(integer) ng4(integer)     Parallele computing is off. Analyzing data using 1 CPU core...        K-fold cross-validation done!!     3 assignment tests completed!!     Results were saved in a 'High_Fst_Locus_Freq.txt' file in the directory.[ FAIL 3 | WARN 0 | SKIP 0 | PASS 39 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test_accuracy.R:8:3'): Calculate assignment accuracy for Monte-Carlo results ──   `plot` has type 'object', not 'list'.   ── Failure ('test_accuracy.R:18:3'): Calculate assignment accuracy for K-fold results ──   `plot` has type 'object', not 'list'.   ── Failure ('test_membership.R:5:3'): Plot membership probability ──────────────   `plot` has type 'object', not 'list'.      [ FAIL 3 | WARN 0 | SKIP 0 | PASS 39 ]   Error: Test failures   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: 1 ERROR