CRAN Package Check Results for Package HTSSIP

Last updated on 2020-08-07 01:49:48 CEST.

Check Details

Version: 1.4.1
Flags: --no-vignettes
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘igraph’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.4.1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘igraph’
     All declared Imports should be used.
Flavors: r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.4.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [53s/53s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     24. base:::withOneRestart(expr, restarts[[1L]])
     25. base:::doWithOneRestart(return(expr), restart)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 102 | SKIPPED: 18 | WARNINGS: 10 | FAILED: 3 ]
     1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)
     2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
     3. Error: HRSIP runs with default (@test-HRSIP.R#3)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.4.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘BD_shifts.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: 'dplyr'
    
    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: phyloseq
    --- finished re-building ‘BD_shifts.Rmd’
    
    --- re-building ‘HTSSIP_intro.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: 'dplyr'
    
    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 ‘HTSSIP_intro.Rmd’
    
    --- re-building ‘HTSSIP_sim.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: 'dplyr'
    
    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 ‘HTSSIP_sim.Rmd’
    
    --- re-building ‘MW_HR_SIP.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: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Loading required namespace: DESeq2
    Failed with error: 'there is no package called 'GenomeInfoDbData''
    Quitting from lines 84-89 (MW_HR_SIP.Rmd)
    Error: processing vignette 'MW_HR_SIP.Rmd' failed with diagnostics:
    there is no package called 'GenomeInfoDbData'
    --- failed re-building ‘MW_HR_SIP.Rmd’
    
    --- re-building ‘beta_diversity_ordinations.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: 'dplyr'
    
    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: phyloseq
    --- finished re-building ‘beta_diversity_ordinations.Rmd’
    
    --- re-building ‘heavy_SIP.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: 'dplyr'
    
    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 ‘heavy_SIP.Rmd’
    
    --- re-building ‘qSIP.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: 'dplyr'
    
    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 ‘qSIP.Rmd’
    
    --- re-building ‘quant_incorp.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: 'dplyr'
    
    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 ‘quant_incorp.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘MW_HR_SIP.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64