CRAN Package Check Results for Package theseus

Last updated on 2020-04-09 09:48:30 CEST.

Check Details

Version: 0.1.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: 'dada2'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [13s/15s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     -- 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     == testthat results ===========================================================
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [11s/17s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘gridExtra’ ‘splancs’ ‘tidyverse’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [19s/21s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/10s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.0
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [13s/14s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [8s/12s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-osx-x86_64

Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘general_usage.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'general_usage.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘general_usage.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘general_usage.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-osx-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [24s/24s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(theseus)
     >
     > test_check("theseus")
     ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
     attempting to coerce non-factor
     Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.1.0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘ShortRead’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-osx-x86_64