CRAN Package Check Results for Package HTSSIP

Last updated on 2020-12-04 00:48:23 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.1 7.93 176.71 184.64 OK --no-vignettes
r-devel-linux-x86_64-debian-gcc 1.4.1 6.74 130.67 137.41 OK --no-vignettes
r-devel-linux-x86_64-fedora-clang 1.4.1 1386.82 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4.1 1309.44 NOTE
r-devel-windows-ix86+x86_64 1.4.1 17.00 160.00 177.00 OK --no-vignettes
r-patched-linux-x86_64 1.4.1 9.11 172.48 181.59 OK --no-vignettes
r-patched-solaris-x86 1.4.1 2608.40 NOTE
r-release-linux-x86_64 1.4.1 8.07 168.62 176.69 OK --no-vignettes
r-release-macos-x86_64 1.4.1 NOTE
r-release-windows-ix86+x86_64 1.4.1 15.00 235.00 250.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.4.1 ERROR
r-oldrel-windows-ix86+x86_64 1.4.1 12.00 443.00 455.00 OK --no-vignettes

Check Details

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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, 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’ [54s/54s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     ERROR (test-HRSIP.R:3:3): HRSIP runs with default
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-delta_BD.R:29:3): delta BD on rep3 dataset
     Warning (test-heavy_SIP.R:7:3): heavy-SIP runs on replicated dataset with default settings
     Warning (test-heavy_SIP.R:7:3): heavy-SIP runs on replicated dataset with default settings
     Warning (test-qSIP_atom_excess.R:41:3): bootstrap iteration is working
    
     [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
     Error: Test failures
     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