CRAN Package Check Results for Package genBart

Last updated on 2020-02-15 01:01:25 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 130.81 406.75 537.56 OK
r-devel-linux-x86_64-debian-gcc 1.0.1 128.66 290.98 419.64 OK
r-devel-linux-x86_64-fedora-clang 1.0.1 562.49 WARN
r-devel-linux-x86_64-fedora-gcc 1.0.1 670.77 NOTE
r-devel-windows-ix86+x86_64 1.0.1 199.00 426.00 625.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.1 210.00 534.00 744.00 ERROR
r-patched-linux-x86_64 1.0.1 130.71 357.18 487.89 OK
r-patched-solaris-x86 1.0.1 1180.80 NOTE
r-release-linux-x86_64 1.0.1 129.81 361.03 490.84 OK
r-release-windows-ix86+x86_64 1.0.1 176.00 388.00 564.00 OK
r-release-osx-x86_64 1.0.1 ERROR
r-oldrel-windows-ix86+x86_64 1.0.1 164.00 367.00 531.00 OK
r-oldrel-osx-x86_64 1.0.1 NOTE

Check Details

Version: 1.0.1
Check: package dependencies
Result: WARN
    Requires orphaned package: ‘clValid’
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
     ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
     ‘statmod’ ‘stringr’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0.1
Check: tests
Result: ERROR
     Running 'testthat.R' [32s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(genBart)
     Welcome to genBart! To get started, it is recommended to walk
     through the vignette. It can be accessed through browseVignettes("genBart").
     >
     > test_check("genBart")
     -- 1. Error: genModelResults outputs correctly for one comparison (@test_genMode
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Backtrace:
     1. DESeq2::results(dds, contrast = c("group", "Active20", "Active0"))
     2. DESeq2:::pvalueAdjustment(...)
     4. S4Vectors:::`$<-`(...)
     6. S4Vectors:::`[[<-`(...)
     10. S4Vectors:::.nextMethod(x, i, value = value)
     12. S4Vectors::setListElement(x, i, value)
     13. S4Vectors:::.append_list_element(x, value, name)
     14. S4Vectors:::.wrap_in_length_one_list_like_object(...)
    
     -- 2. Error: genModelResults outputs correctly for multiple comparisons (@test_g
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Backtrace:
     1. DESeq2::results(dds, contrast = c("group", "Active20", "Active0"))
     2. DESeq2:::pvalueAdjustment(...)
     4. S4Vectors:::`$<-`(...)
     6. S4Vectors:::`[[<-`(...)
     10. S4Vectors:::.nextMethod(x, i, value = value)
     12. S4Vectors::setListElement(x, i, value)
     13. S4Vectors:::.append_list_element(x, value, name)
     14. S4Vectors:::.wrap_in_length_one_list_like_object(...)
    
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to controls..."
     [1] "clustering genes from baseline samples normalized to mean..."
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to baseline..."
     [1] "clustering genes from baseline samples normalized to mean..."
     [1] "clustering genes from baseline samples normalized to controls..."
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to controls..."
     [1] "clustering genes from all samples normalized to baseline..."
     == testthat results ===========================================================
     [ OK: 134 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
     1. Error: genModelResults outputs correctly for one comparison (@test_genModelResults.R#66)
     2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#87)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 1.0.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [9s/9s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     [1] "clustering genes from baseline samples normalized to mean..."
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to baseline..."
     [1] "clustering genes from baseline samples normalized to mean..."
     [1] "clustering genes from baseline samples normalized to controls..."
     [1] "clustering genes from all samples normalized to mean..."
     [1] "clustering genes from all samples normalized to controls..."
     [1] "clustering genes from all samples normalized to baseline..."
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 134 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
     1. Error: genModelResults outputs correctly for one comparison (@test_genModelResults.R#64)
     2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-osx-x86_64