CRAN Package Check Results for Package ActiveDriverWGS

Last updated on 2020-04-09 22:50:13 CEST.

Check Details

Version: 1.0.1
Check: tests
Result: ERROR
     Running 'testthat.R' [6s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(ActiveDriverWGS)
     >
     > test_check("ActiveDriverWGS")
     -- 1. Error: (unknown) (@test_ADWGS_test.R#3) ---------------------------------
     package 'S4Vectors' could not be loaded
     Backtrace:
     1. base::library(GenomicRanges)
     2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
    
     -- 2. Error: (unknown) (@test_ActiveDriverWGS.R#3) ----------------------------
     package 'S4Vectors' could not be loaded
     Backtrace:
     1. base::library(GenomicRanges)
     2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
    
     reversing 0 positions
     -- 3. Error: (unknown) (@test_format_muts.R#7) --------------------------------
     .onLoad failed in loadNamespace() for 'S4Vectors', details:
     call: validObject(.Object)
     error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
     Backtrace:
     1. ActiveDriverWGS::format_muts(cll_mutations[1:10, ])
     2. ActiveDriverWGS:::.get_3n_context_of_mutations(mutations)
     3. GenomicRanges::GRanges
     4. base::getExportedValue(pkg, name)
     5. base::asNamespace(ns)
     6. base::getNamespace(ns)
     7. base::loadNamespace(name)
     9. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     10. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 4. Failure: mutations are formatted properly (@test_input_format.R#61) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "Only the 22 autosomal and 2 sex chromosomes may be used at this time. Note that chr23 should be formatted as chrX and chr24 should be formatted as chrY"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 5. Failure: mutations are formatted properly (@test_input_format.R#68) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "Reference and alternate alleles must be A, T, C or G"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 6. Failure: mutations are formatted properly (@test_input_format.R#74) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "Reference and alternate alleles must be A, T, C or G"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 7. Failure: mutations are formatted properly (@test_input_format.R#81) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "pos1 and pos2 must be numeric"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 8. Failure: mutations are formatted properly (@test_input_format.R#87) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "pos1 and pos2 must be numeric"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 9. Failure: mutations are formatted properly (@test_input_format.R#95) -----
     `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
     Expected match: "patient identifier must be a string"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 10. Failure: elements are formatted properly (@test_input_format.R#112) ----
     `ActiveDriverWGS(elements = as.matrix(cancer_genes), mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "elements must be a data frame"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 11. Failure: elements are formatted properly (@test_input_format.R#117) ----
     `ActiveDriverWGS(elements = cancer_genes[, 1:3], mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "elements must contain the following columns: chr, start, end & id"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 12. Failure: elements are formatted properly (@test_input_format.R#124) ----
     `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "elements may not contain missing values"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 13. Failure: elements are formatted properly (@test_input_format.R#130) ----
     `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "duplicated elements are present. please review your format"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 14. Failure: elements are formatted properly (@test_input_format.R#137) ----
     `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "start and end must be numeric"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 15. Failure: elements are formatted properly (@test_input_format.R#144) ----
     `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
     Expected match: "element identifier must be a string"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 16. Failure: sites are formatted properly (@test_input_format.R#152) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "sites must be a data frame"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 17. Failure: sites are formatted properly (@test_input_format.R#158) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "sites must contain the following columns: chr, start, end & id"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 18. Failure: sites are formatted properly (@test_input_format.R#167) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "sites may not contain missing values"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 19. Failure: sites are formatted properly (@test_input_format.R#174) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "duplicated sites are present. please review your format"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 20. Failure: sites are formatted properly (@test_input_format.R#182) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "start and end must be numeric"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
     -- 21. Failure: sites are formatted properly (@test_input_format.R#190) -------
     `ActiveDriverWGS(...)` threw an error with unexpected message.
     Expected match: "site identifier must be a string"
     Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n call: validObject(.Object)\n error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
     Backtrace:
     1. testthat::expect_error(...)
     6. ActiveDriverWGS::ActiveDriverWGS(...)
     8. BSgenome::seqnames
     9. base::getExportedValue(pkg, name)
     10. base::asNamespace(ns)
     11. base::getNamespace(ns)
     12. base::loadNamespace(name)
     14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     15. base:::runHook(".onLoad", env, package.lib, package)
    
    
     1189 Rows :: Processing row 100 200 300 400 500 600 700 800 900 1000 1100
     Preparing Elements Complete
     RM 0 lines
    
     5 Rows :: Processing row
     5 Rows :: Processing row
     5 Rows :: Processing row == testthat results ===========================================================
     [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 21 ]
     1. Error: (unknown) (@test_ADWGS_test.R#3)
     2. Error: (unknown) (@test_ActiveDriverWGS.R#3)
     3. Error: (unknown) (@test_format_muts.R#7)
     4. Failure: mutations are formatted properly (@test_input_format.R#61)
     5. Failure: mutations are formatted properly (@test_input_format.R#68)
     6. Failure: mutations are formatted properly (@test_input_format.R#74)
     7. Failure: mutations are formatted properly (@test_input_format.R#81)
     8. Failure: mutations are formatted properly (@test_input_format.R#87)
     9. Failure: mutations are formatted properly (@test_input_format.R#95)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'ActiveDriverWGSR.Rmd' using rmarkdown
    Quitting from lines 109-116 (ActiveDriverWGSR.Rmd)
    Error: processing vignette 'ActiveDriverWGSR.Rmd' failed with diagnostics:
    .onLoad failed in loadNamespace() for 'S4Vectors', details:
     call: validObject(.Object)
     error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
    --- failed re-building 'ActiveDriverWGSR.Rmd'
    
    SUMMARY: processing the following file failed:
     'ActiveDriverWGSR.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavors: r-patched-osx-x86_64, r-release-osx-x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-osx-x86_64