CRAN Package Check Results for Maintainer ‘Alex M Chubaty <alex.chubaty at gmail.com>’

Last updated on 2019-12-16 00:49:21 CET.

Package ERROR WARN NOTE OK
fpCompare 13
grainscape 5 8
SpaDES 2 11
SpaDES.addins 5 8
SpaDES.core 3 10
SpaDES.tools 1 12

Package fpCompare

Current CRAN status: OK: 13

Package grainscape

Current CRAN status: WARN: 5, OK: 8

Version: 0.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'MPG_algorithm.Rmd' using rmarkdown
    --- finished re-building 'MPG_algorithm.Rmd'
    
    --- re-building 'grainscape_vignette.Rmd' using rmarkdown
    ! Misplaced \crcr.
    \endtabular ->\crcr
     \egroup \egroup $\egroup
    l.145 \maketitle
    
    Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
    Failed to compile grainscape_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info.
    --- failed re-building 'grainscape_vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'grainscape_vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'MPG_algorithm.Rmd' using rmarkdown
    --- finished re-building 'MPG_algorithm.Rmd'
    
    --- re-building 'grainscape_vignette.Rmd' using rmarkdown
    ! Misplaced \crcr.
    \endtabular ->\crcr
     \egroup \egroup $\egroup
    l.143 \maketitle
    
    Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
    Failed to compile grainscape_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info.
    --- failed re-building 'grainscape_vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'grainscape_vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'MPG_algorithm.Rmd' using rmarkdown
    --- finished re-building 'MPG_algorithm.Rmd'
    
    --- re-building 'grainscape_vignette.Rmd' using rmarkdown
    ! Misplaced \crcr.
    \endtabular ->\crcr
     \egroup \egroup $\egroup
    l.143 \maketitle
    
    Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
    Failed to compile grainscape_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info.
    --- failed re-building 'grainscape_vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'grainscape_vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.4.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    ! Misplaced \crcr.
    \endtabular ->\crcr
     \egroup \egroup $\egroup
    l.143 \maketitle
    
    Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
    Failed to compile grainscape_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package SpaDES

Current CRAN status: WARN: 2, OK: 11

Version: 2.0.4
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: 2.0.4
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: 2.0.4
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: 2.0.4
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: 2.0.4
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: 2.0.4
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: 2.0.4
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: 2.0.4
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

Package SpaDES.addins

Current CRAN status: NOTE: 5, OK: 8

Version: 0.1.2
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘devtools’ ‘rstudioapi’
     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-osx-x86_64, r-oldrel-osx-x86_64

Package SpaDES.core

Current CRAN status: WARN: 3, OK: 10

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/RtmpKlaWly/working_dir/RtmpPkay6y/raster'
     reproducible.cachePath = '/tmp/RtmpKlaWly/working_dir/RtmpPkay6y/reproducible/cache'
     spades.inputPath = '/tmp/RtmpZ2aW.M/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpZ2aW.M/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/RtmpKlaWly/working_dir/Rtmphvaq7D/raster'
     reproducible.cachePath = '/tmp/RtmpKlaWly/working_dir/Rtmphvaq7D/reproducible/cache'
     spades.inputPath = '/tmp/RtmpZ2aW.M/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpZ2aW.M/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

Package SpaDES.tools

Current CRAN status: ERROR: 1, OK: 12

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘test-all.R’ [6m/11m]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.tools")
     Loading required package: SpaDES.tools
     ── 1. Failure: spread2 tests (@test-spread2.R#183) ────────────────────────────
     difftime(afterTime, beforeTime, units = "sec") < 1 isn't true.
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 1057 | SKIPPED: 5 | WARNINGS: 0 | FAILED: 1 ]
     1. Failure: spread2 tests (@test-spread2.R#183)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc