CRAN Package Check Results for Package Signac

Last updated on 2021-03-04 00:48:10 CET.

Check Details

Version: 1.1.1
Check: package dependencies
Result: NOTE
    Imports includes 31 non-default packages.
    Importing from so many packages makes the package vulnerable to any of
    them becoming unavailable. Move as many as possible to Suggests and
    use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: 'SeuratObject'
     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

Version: 1.1.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'chromVAR', 'TFBSTools', 'motifmatchr'
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘TFBSTools’, ‘motifmatchr’, ‘chromVAR’
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘ggbio’
    
    Packages suggested but not available for checking:
     'chromVAR', 'TFBSTools', 'motifmatchr'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-x86_64

Version: 1.1.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     'ggbio', 'biovizBase', 'AnnotationFilter'
    
    Packages suggested but not available for checking:
     'chromVAR', 'TFBSTools', 'motifmatchr'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: whether the namespace can be unloaded cleanly
Result: WARN
    ---- unloading
    Error in .mergeMethodsTable(generic, mtable, tt, attach) :
     trying to get slot "defined" from an object of a basic class ("environment") with no slots
    Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
    Execution halted
Flavors: r-oldrel-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.1
Check: for code/documentation mismatches
Result: WARN
    Found more than one class "Assay" in cache; using the first, from namespace 'Seurat'
    Also defined by 'SeuratObject'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.1.1
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'Signac-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: Annotation
    > ### Title: Annotation
    > ### Aliases: Annotation Annotation<- Annotation.ChromatinAssay
    > ### Annotation.Seurat Annotation<-.ChromatinAssay Annotation<-.Seurat
    >
    > ### ** Examples
    >
    > genes <- Annotation(atac_small)
    > Annotation(atac_small[["peaks"]]) <- genes
    Error in `[[<-`(`*tmp*`, "peaks", value = new("ChromatinAssay", ranges = new("GRanges", :
     [[<- defined for objects of type "S4" only for subclasses of environment
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.1.1
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'Signac-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: Annotation
    > ### Title: Annotation
    > ### Aliases: Annotation Annotation<- Annotation.ChromatinAssay
    > ### Annotation.Seurat Annotation<-.ChromatinAssay Annotation<-.Seurat
    >
    > ### ** Examples
    >
    > genes <- Annotation(atac_small)
    > Annotation(atac_small[["peaks"]]) <- genes
    Error in `[[<-`(`*tmp*`, "peaks", value = new("ChromatinAssay", ranges = new("GRanges", :
     [[<- defined for objects of type "S4" only for subclasses of environment
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.1.1
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [33s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Signac)
     >
     > test_check("Signac")
     == Failed tests ================================================================
     -- Error (test-preprocessing.R:23:3): DownsampleFeatures works -----------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. \-Signac::DownsampleFeatures(object = atac_small, n = 5, verbose = FALSE) test-preprocessing.R:23:2
     2. +-Seurat::`VariableFeatures<-`(...)
     3. \-Seurat:::`VariableFeatures<-.Seurat`(...)
     -- Error (test-preprocessing.R:37:3): FindTopFeatures works --------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Seurat::`VariableFeatures<-`(`*tmp*`, value = NULL) test-preprocessing.R:37:2
     2. \-Seurat:::`VariableFeatures<-.Seurat`(`*tmp*`, value = NULL)
     -- Error (test-preprocessing.R:51:3): FRiP works -------------------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. \-Signac::FRiP(object = atac_small, assay = "peaks", total.fragments = "fragments") test-preprocessing.R:51:2
     2. +-Seurat::AddMetaData(object = object, metadata = frip, col.name = col.name)
     3. \-Seurat:::AddMetaData.Seurat(...)
     4. \-Seurat:::.AddMetaData(object = object, metadata = metadata, col.name = col.name)
     -- Error (test-preprocessing.R:91:3): NucleosomeSignal works -------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Signac::`Fragments<-`(...) test-preprocessing.R:91:2
     2. \-Signac:::`Fragments<-.Seurat`(...)
     -- Error (test_fragments.R:126:3): SplitFragments works ------------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Signac::`Fragments<-`(...) test_fragments.R:126:2
     2. \-Signac:::`Fragments<-.Seurat`(...)
    
     [ FAIL 5 | WARN 0 | SKIP 0 | PASS 34 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.1.1
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [37s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Signac)
     >
     > test_check("Signac")
     == Failed tests ================================================================
     -- Error (test-preprocessing.R:23:3): DownsampleFeatures works -----------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. \-Signac::DownsampleFeatures(object = atac_small, n = 5, verbose = FALSE) test-preprocessing.R:23:2
     2. +-Seurat::`VariableFeatures<-`(...)
     3. \-Seurat:::`VariableFeatures<-.Seurat`(...)
     -- Error (test-preprocessing.R:37:3): FindTopFeatures works --------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Seurat::`VariableFeatures<-`(`*tmp*`, value = NULL) test-preprocessing.R:37:2
     2. \-Seurat:::`VariableFeatures<-.Seurat`(`*tmp*`, value = NULL)
     -- Error (test-preprocessing.R:51:3): FRiP works -------------------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. \-Signac::FRiP(object = atac_small, assay = "peaks", total.fragments = "fragments") test-preprocessing.R:51:2
     2. +-Seurat::AddMetaData(object = object, metadata = frip, col.name = col.name)
     3. \-Seurat:::AddMetaData.Seurat(...)
     4. \-Seurat:::.AddMetaData(object = object, metadata = metadata, col.name = col.name)
     -- Error (test-preprocessing.R:91:3): NucleosomeSignal works -------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Signac::`Fragments<-`(...) test-preprocessing.R:91:2
     2. \-Signac:::`Fragments<-.Seurat`(...)
     -- Error (test_fragments.R:126:3): SplitFragments works ------------------------
     Error: [[<- defined for objects of type "S4" only for subclasses of environment
     Backtrace:
     x
     1. +-Signac::`Fragments<-`(...) test_fragments.R:126:2
     2. \-Signac:::`Fragments<-.Seurat`(...)
    
     [ FAIL 5 | WARN 0 | SKIP 0 | PASS 34 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64