CRAN Package Check Results for Package genBart

Last updated on 2020-01-20 01:50:21 CET.

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' [25s]
    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
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Backtrace:
     1. DESeq2::DESeqDataSetFromMatrix(dat, colData = design2, design = ~group)
     2. DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     3. S4Vectors::DataFrame(...)
     4. methods::is(listData[[1L]], getClass("Annotated"))
    
     -- 2. Error: genModelResults outputs correctly for multiple comparisons (@test_g
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Backtrace:
     1. DESeq2::DESeqDataSetFromMatrix(dat, colData = design2, design = ~group)
     2. DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     3. S4Vectors::DataFrame(...)
     4. methods::is(listData[[1L]], getClass("Annotated"))
    
     [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#64)
     2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.0.1
Check: tests
Result: ERROR
     Running 'testthat.R' [24s]
    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
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Backtrace:
     1. DESeq2::DESeqDataSetFromMatrix(dat, colData = design2, design = ~group)
     2. DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     3. S4Vectors::DataFrame(...)
     4. methods::is(listData[[1L]], getClass("Annotated"))
    
     -- 2. Error: genModelResults outputs correctly for multiple comparisons (@test_g
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Backtrace:
     1. DESeq2::DESeqDataSetFromMatrix(dat, colData = design2, design = ~group)
     2. DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     3. S4Vectors::DataFrame(...)
     4. methods::is(listData[[1L]], getClass("Annotated"))
    
     [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#64)
     2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85)
    
     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