CRAN Package Check Results for Package PLNmodels

Last updated on 2019-06-18 01:48:48 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.2 104.76 364.07 468.83 OK
r-devel-linux-x86_64-debian-gcc 0.9.2 80.80 276.81 357.61 OK
r-devel-linux-x86_64-fedora-clang 0.9.2 578.04 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.2 552.55 OK
r-devel-windows-ix86+x86_64 0.9.2 258.00 721.00 979.00 OK
r-patched-linux-x86_64 0.9.2 93.10 354.31 447.41 OK
r-patched-solaris-x86 0.9.2 770.50 WARN
r-release-linux-x86_64 0.9.2 97.41 353.24 450.65 OK
r-release-windows-ix86+x86_64 0.9.2 206.00 593.00 799.00 OK
r-release-osx-x86_64 0.9.2 ERROR
r-oldrel-windows-ix86+x86_64 0.9.2 170.00 624.00 794.00 OK
r-oldrel-osx-x86_64 0.9.2 WARN

Check Details

Version: 0.9.2
Check: installed package size
Result: NOTE
     installed size is 9.3Mb
     sub-directories of 1Mb or more:
     doc 1.6Mb
     libs 6.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-oldrel-osx-x86_64

Version: 0.9.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘Import_data.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.
    1 samples were dropped from the abundance matrix for lack of associated covariates.
    --- finished re-building ‘Import_data.Rmd’
    
    --- re-building ‘PLN.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.
    corrplot 0.84 loaded
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:gridExtra':
    
     combine
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Warning: Transformation introduced infinite values in continuous x-axis
    Quitting from lines 186-190 (PLN.Rmd)
    Error: processing vignette 'PLN.Rmd' failed with diagnostics:
    unused argument (options = options)
    --- failed re-building ‘PLN.Rmd’
    
    --- re-building ‘PLNLDA.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.
    Warning in kable_markdown(x = c("3302930", "3307296", "3348069", "3394105", :
     The table should have a header (column names)
    Warning in kable_markdown(x = c("Che", "Hyc", "Hym", "Hys", "Psy", "Aga", :
     The table should have a header (column names)
    Warning: glm.fit: algorithm did not converge
    Warning: glm.fit: fitted rates numerically 0 occurred
    --- finished re-building ‘PLNLDA.Rmd’
    
    --- re-building ‘PLNPCA.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.
    corrplot 0.84 loaded
    Warning in kable_markdown(x = c("Che", "Hyc", "Hym", "Hys", "Psy", "Aga", :
     The table should have a header (column names)
    Warning in kable_markdown(x = c("-1.606816", "3.835259", "7.562147", "6.244162", :
     The table should have a header (column names)
    Warning: Transformation introduced infinite values in continuous x-axis
    Warning: Removed 584 rows containing missing values (geom_point).
    --- finished re-building ‘PLNPCA.Rmd’
    
    --- re-building ‘PLNnetwork.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.
    Warning: Transformation introduced infinite values in continuous x-axis
    Warning: Removed 588 rows containing missing values (geom_point).
    --- finished re-building ‘PLNnetwork.Rmd’
    
    --- re-building ‘Trichoptera.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.
    --- finished re-building ‘Trichoptera.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘PLN.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.9.2
Check: package dependencies
Result: ERROR
    Packages required but not available: 'biomformat', 'phyloseq'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 0.9.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    1 samples were dropped from the abundance matrix for lack of associated covariates.
    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.
    corrplot 0.84 loaded
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:gridExtra':
    
     combine
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Warning: Transformation introduced infinite values in continuous x-axis
    Quitting from lines 186-190 (PLN.Rmd)
    Error: processing vignette 'PLN.Rmd' failed with diagnostics:
    unused argument (options = options)
    Execution halted
Flavor: r-oldrel-osx-x86_64