CRAN Package Check Results for Package assignPOP

Last updated on 2020-02-20 14:47:35 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.7 19.82 139.79 159.61 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.7 17.96 111.99 129.95 OK
r-devel-linux-x86_64-fedora-clang 1.1.7 198.49 OK
r-devel-linux-x86_64-fedora-gcc 1.1.7 198.44 OK
r-devel-windows-ix86+x86_64 1.1.7 40.00 140.00 180.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.1.7 60.00 193.00 253.00 OK
r-patched-linux-x86_64 1.1.7 16.28 122.97 139.25 OK
r-patched-solaris-x86 1.1.7 242.30 OK
r-release-linux-x86_64 1.1.7 17.13 122.97 140.10 OK
r-release-windows-ix86+x86_64 1.1.7 33.00 137.00 170.00 OK
r-release-osx-x86_64 1.1.7 OK
r-oldrel-windows-ix86+x86_64 1.1.7 26.00 136.00 162.00 OK
r-oldrel-osx-x86_64 1.1.7 OK

Check Details

Version: 1.1.7
Check: tests
Result: ERROR
     Running 'testthat.R' [10s/11s]
    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.-- 1. Error: Calculate assignment accuracy for Monte-Carlo results (@test_accura
     object 'checkTrainInds' not found
     Backtrace:
     1. assignPOP::accuracy.plot(AccuMC)
    
    
     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.
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     ################ assignPOP v1.1.7 ################
    
     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...
     -- 2. Error: Perfrom Monte-Calro cross-validation - loci.sample=random (@test_as
     Need numeric dependent variable for regression.
     Backtrace:
     1. assignPOP::assign.MC(...)
     3. e1071:::svm.formula(...)
     4. e1071:::svm.default(x, y, scale = scale, ..., na.action = na.action)
    
    
     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...
     -- 3. Error: Perfrom Monte-Calro cross-validation - model=naiveBayes (@test_assi
     arguments imply differing number of rows: 12, 0
     Backtrace:
     1. assignPOP::assign.MC(...)
     2. base::cbind(...)
     3. base::cbind(deparse.level, ...)
     4. base::data.frame(..., check.names = FALSE)
    
    
     Parallele computing is off. Analyzing data using 1 CPU core...
     -- 4. Error: Perfrom Monte-Calro cross-validation - model=tree (@test_assignMC.R
     type "class" only for classification trees
     Backtrace:
     1. assignPOP::assign.MC(...)
     3. tree:::predict.tree(tree.model, testSetData_PC, type = "class")
    
    
     Parallele computing is off. Analyzing data using 1 CPU core...
     -- 5. Error: Perfrom Monte-Calro cross-validation - model=randomForest (@test_as
     non-numeric argument to binary operator
     Backtrace:
     1. assignPOP::assign.MC(...)
     3. randomForest:::randomForest.formula(...)
     4. randomForest:::randomForest.default(m, y, ...)
    
    
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     ################ assignPOP v1.1.7 ################
    
     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
    
    
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     ################ assignPOP v1.1.7 ################
    
     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...-- 6. Error: Perform one-time assignment test on unknown individuals (@test_assi
     Need numeric dependent variable for regression.
     Backtrace:
     1. assignPOP::assign.X(...)
     3. e1071:::svm.formula(...)
     4. e1071:::svm.default(x, y, scale = scale, ..., na.action = na.action)
    
    
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     ################ assignPOP v1.1.7 ################
    
     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...
     -- 7. Error: Perform K-fold cross-validation, genetic data (@test_assignkfold.R#
     Need numeric dependent variable for regression.
     Backtrace:
     1. assignPOP::assign.kfold(...)
     3. e1071:::svm.formula(...)
     4. e1071:::svm.default(x, y, scale = scale, ..., na.action = na.action)
    
     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...
     -- 8. Error: Perform K-fold cross-validation, integrated data (@test_assignkfold
     Need numeric dependent variable for regression.
     Backtrace:
     1. assignPOP::assign.kfold(...)
     3. e1071:::svm.formula(...)
     4. e1071:::svm.default(x, y, scale = scale, ..., na.action = na.action)
    
    
     Convert sample ID to factor.
    
     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.== testthat results ===========================================================
     [ OK: 27 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 8 ]
     1. Error: Calculate assignment accuracy for Monte-Carlo results (@test_accuracy.R#7)
     2. Error: Perfrom Monte-Calro cross-validation - loci.sample=random (@test_assignMC.R#6)
     3. Error: Perfrom Monte-Calro cross-validation - model=naiveBayes (@test_assignMC.R#27)
     4. Error: Perfrom Monte-Calro cross-validation - model=tree (@test_assignMC.R#34)
     5. Error: Perfrom Monte-Calro cross-validation - model=randomForest (@test_assignMC.R#41)
     6. Error: Perform one-time assignment test on unknown individuals (@test_assignX.R#7)
     7. Error: Perform K-fold cross-validation, genetic data (@test_assignkfold.R#6)
     8. Error: Perform K-fold cross-validation, integrated data (@test_assignkfold.R#15)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang