CRAN Package Check Results for Package BaseSet

Last updated on 2021-03-03 12:46:58 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.14 OK
r-devel-linux-x86_64-debian-gcc 0.0.14 7.13 205.10 212.23 OK
r-devel-linux-x86_64-fedora-clang 0.0.14 369.27 OK
r-devel-linux-x86_64-fedora-gcc 0.0.14 365.13 OK
r-devel-windows-ix86+x86_64 0.0.14 21.00 361.00 382.00 OK
r-patched-linux-x86_64 0.0.14 8.59 272.02 280.61 OK
r-patched-solaris-x86 0.0.14 455.10 OK
r-release-linux-x86_64 0.0.14 9.52 277.24 286.76 OK
r-release-macos-x86_64 0.0.14 WARN
r-release-windows-ix86+x86_64 0.0.14 17.00 263.00 280.00 OK
r-oldrel-macos-x86_64 0.0.14 ERROR
r-oldrel-windows-ix86+x86_64 0.0.14 16.00 243.00 259.00 ERROR

Check Details

Version: 0.0.14
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘reactome.db’
Flavor: r-release-macos-x86_64

Version: 0.0.14
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘advanced.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:BaseSet':
    
     union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Loading required package: AnnotationDbi
    Loading required package: stats4
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    The following objects are masked from 'package:dplyr':
    
     combine, intersect, setdiff, union
    
    The following object is masked from 'package:BaseSet':
    
     union
    
    The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    Loading required package: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:dplyr':
    
     first, rename
    
    The following object is masked from 'package:BaseSet':
    
     active
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    
    Attaching package: 'IRanges'
    
    The following objects are masked from 'package:dplyr':
    
     collapse, desc, slice
    
    
    Attaching package: 'AnnotationDbi'
    
    The following object is masked from 'package:dplyr':
    
     select
    
    The following object is masked from 'package:BaseSet':
    
     select
    
    
    
    Quitting from lines 235-251 (advanced.Rmd)
    Error: processing vignette 'advanced.Rmd' failed with diagnostics:
    there is no package called 'reactome.db'
    --- failed re-building ‘advanced.Rmd’
    
    --- re-building ‘basic.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘basic.Rmd’
    
    --- re-building ‘fuzzy.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:BaseSet':
    
     union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘fuzzy.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘advanced.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 0.0.14
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GO.db', 'org.Hs.eg.db', 'reactome.db'
Flavor: r-oldrel-macos-x86_64

Version: 0.0.14
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/0s]
     Running ‘testthat.R’ [9s/9s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     1/1 mismatches
     [1] 7 - 2 == 5
     ── Failure (test-element_size.R:19:5): element_size works ──────────────────────
     out$size not equal to c(0, 1).
     Lengths differ: 7 is not 2
     ── Failure (test-pull.R:29:5): pull works ──────────────────────────────────────
     `out` not equal to c("a", "b", "a2", "b2").
     'current' is not a factor
     ── Failure (test-pull.R:59:5): pull uses active ────────────────────────────────
     `out` not equal to c("a", "b", "a2", "b2").
     'current' is not a factor
    
     [ FAIL 4 | WARN 0 | SKIP 0 | PASS 407 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 0.0.14
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘advanced.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:BaseSet':
    
     union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 53-60 (advanced.Rmd)
    Error: processing vignette 'advanced.Rmd' failed with diagnostics:
    there is no package called 'org.Hs.eg.db'
    --- failed re-building ‘advanced.Rmd’
    
    --- re-building ‘basic.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘basic.Rmd’
    
    --- re-building ‘fuzzy.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'BaseSet'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:BaseSet':
    
     union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘fuzzy.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘advanced.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 0.0.14
Check: tests
Result: ERROR
     Running 'spelling.R' [0s]
     Running 'testthat.R' [10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(BaseSet)
    
     Attaching package: 'BaseSet'
    
     The following object is masked from 'package:stats':
    
     filter
    
     The following object is masked from 'package:base':
    
     union
    
     >
     > test_check("BaseSet")
     == Failed tests ================================================================
     -- Failure (test-element_size.R:18:5): element_size works ----------------------
     nrow(out) not equal to 2L.
     1/1 mismatches
     [1] 7 - 2 == 5
     -- Failure (test-element_size.R:19:5): element_size works ----------------------
     out$size not equal to c(0, 1).
     Lengths differ: 7 is not 2
     -- Failure (test-pull.R:29:5): pull works --------------------------------------
     `out` not equal to c("a", "b", "a2", "b2").
     'current' is not a factor
     -- Failure (test-pull.R:59:5): pull uses active --------------------------------
     `out` not equal to c("a", "b", "a2", "b2").
     'current' is not a factor
    
     [ FAIL 4 | WARN 0 | SKIP 0 | PASS 407 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64