CRAN Package Check Results for Package SpaDES.core

Last updated on 2020-01-20 01:50:36 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.2.7	53.74	560.11	613.85	OK
r-devel-linux-x86_64-debian-gcc	0.2.7	40.54	446.72	487.26	OK
r-devel-linux-x86_64-fedora-clang	0.2.7			630.67	OK
r-devel-linux-x86_64-fedora-gcc	0.2.7			593.73	OK
r-devel-windows-ix86+x86_64	0.2.7	116.00	611.00	727.00	OK
r-devel-windows-ix86+x86_64-gcc8	0.2.7	86.00	493.00	579.00	OK
r-patched-linux-x86_64	0.2.7	48.87	477.42	526.29	OK
r-patched-solaris-x86	0.2.7			772.40	WARN
r-release-linux-x86_64	0.2.7	48.60	455.07	503.67	OK
r-release-windows-ix86+x86_64	0.2.7	92.00	525.00	617.00	OK
r-release-osx-x86_64	0.2.7				WARN
r-oldrel-windows-ix86+x86_64	0.2.7	45.00	347.00	392.00	OK
r-oldrel-osx-x86_64	0.2.7				WARN

Check Details

Version: 0.2.7
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘i-introduction.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 ‘i-introduction.Rmd’

    --- re-building ‘ii-modules.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: 'igraph'

    The following objects are masked from 'package:stats':

     decompose, spectrum

    The following object is masked from 'package:base':

     union

    Loading required package: quickPlot
    Loading required package: reproducible

    Attaching package: 'SpaDES.core'

    The following objects are masked from 'package:stats':

     end, start

    The following object is masked from 'package:utils':

     citation

    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils

    Attaching package: 'RandomFields'

    The following object is masked from 'package:RandomFieldsUtils':

     RFoptions

    Setting:
     options(
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/tmp/Rtmpc0aWE5/working_dir/Rtmpdza4iT/raster'
     reproducible.cachePath = '/tmp/Rtmpc0aWE5/working_dir/Rtmpdza4iT/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp2yaa8t/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp2yaa8t/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 376-380 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    --- failed re-building ‘ii-modules.Rmd’

    --- re-building ‘iii-cache.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.
    Loading required package: sp

    Attaching package: 'raster'

    The following object is masked from 'package:magrittr':

     extract

    Loading required package: quickPlot

    Attaching package: 'SpaDES.core'

    The following objects are masked from 'package:stats':

     end, start

    The following object is masked from 'package:utils':

     citation

    Setting:
     options(
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/tmp/Rtmpc0aWE5/working_dir/RtmpgrayYY/raster'
     reproducible.cachePath = '/tmp/Rtmpc0aWE5/working_dir/RtmpgrayYY/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp2yaa8t/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp2yaa8t/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    --- finished re-building ‘iii-cache.Rmd’

    --- re-building ‘iv-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.
    --- finished re-building ‘iv-advanced.Rmd’

    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.7
Check: dependencies in R code
Result: NOTE
No protocol specified
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: replacement functions
Result: WARN
    No protocol specified
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: foreign function calls
Result: NOTE
    No protocol specified
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: R code for possible problems
Result: NOTE
No protocol specified
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: for missing documentation entries
Result: WARN
    No protocol specified
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.7
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘i-introduction.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 ‘i-introduction.Rmd’

    --- re-building ‘ii-modules.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: 'igraph'

    The following objects are masked from 'package:stats':

     decompose, spectrum

    The following object is masked from 'package:base':

     union

    Loading required package: quickPlot
    Loading required package: reproducible
    No protocol specified
    No protocol specified
    Warning in fun(libname, pkgname) : couldn't connect to display ":0"

    Attaching package: 'SpaDES.core'

    The following objects are masked from 'package:stats':

     end, start

    The following object is masked from 'package:utils':

     citation

    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils

    Attaching package: 'RandomFields'

    The following object is masked from 'package:RandomFieldsUtils':

     RFoptions

    Setting:
     options(
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/private/tmp/Rtmpyen7pg/raster'
     reproducible.cachePath = '/private/tmp/Rtmpyen7pg/reproducible/cache'
     spades.inputPath = '/private/tmp/RtmpUhRq7g/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpUhRq7g/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 376-380 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘ii-modules.Rmd’

    --- re-building ‘iii-cache.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.
    Loading required package: sp

    Attaching package: 'raster'

    The following object is masked from 'package:magrittr':

     extract

    Loading required package: quickPlot
    No protocol specified
    No protocol specified

    Attaching package: 'SpaDES.core'

    The following objects are masked from 'package:stats':

     end, start

    The following object is masked from 'package:utils':

     citation

    Setting:
     options(
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/private/tmp/RtmpAaEMpb/raster'
     reproducible.cachePath = '/private/tmp/RtmpAaEMpb/reproducible/cache'
     spades.inputPath = '/private/tmp/RtmpUhRq7g/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpUhRq7g/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    --- finished re-building ‘iii-cache.Rmd’

    --- re-building ‘iv-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.
    --- finished re-building ‘iv-advanced.Rmd’

    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2.7
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Attaching package: 'RandomFields'

    The following object is masked from 'package:RandomFieldsUtils':

     RFoptions

    Setting:
     options(
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/private/tmp/RtmpA6jyhK/raster'
     reproducible.cachePath = '/private/tmp/RtmpA6jyhK/reproducible/cache'
     spades.inputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 376-380 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-oldrel-osx-x86_64