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

Last updated on 2019-07-24 00:47:52 CEST.

Package ERROR WARN NOTE OK
fpCompare 12
SpaDES 12
SpaDES.addins 5 7
SpaDES.core 2 2 8
SpaDES.tools 12

Package fpCompare

Current CRAN status: OK: 12

Package SpaDES

Current CRAN status: OK: 12

Package SpaDES.addins

Current CRAN status: NOTE: 5, OK: 7

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: ERROR: 2, WARN: 2, OK: 8

Additional issues

rcnst

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘test-all.R’ [221s/279s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     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
    
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Scx05H"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Scx05H"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Scx05H"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Scx05H"
     Using cached copy of .inputObjects event in test module.
     ── 1. Error: check all examples (@test-examples.R#11) ─────────────────────────
     cannot open the connection
     1: test_examples(path = "../../man") at testthat/test-examples.R:11
     2: test_examples_source(path) %||% test_examples_installed(env_test$package)
     3: test_examples_installed(env_test$package)
     4: lapply(Rd, test_rd)
     5: FUN(X[[i]], ...)
     6: test_example(attr(rd, "Rdfile"))
     7: tools::Rd2ex(path, ex_path)
     8: prepare_Rd(Rd, defines = defines, stages = stages, ...)
     9: eval(substitute(parse_Rd(f, encoding = enc, fragment = frag, ...), list(f = Rd, enc = encoding,
     frag = fragment)))
     10: eval(substitute(parse_Rd(f, encoding = enc, fragment = frag, ...), list(f = Rd, enc = encoding,
     frag = fragment)))
     11: parse_Rd("/home/hornik/tmp/scratch/Rtmp4HRlYa/R.INSTALL3295aea8853/SpaDES.core/man/Copy.Rd",
     encoding = "unknown", fragment = FALSE, ...)
     12: readLines(file, warn = FALSE)
     13: file(con, "r")
    
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/Oaxx2G"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/nz4yC8"
     [1] "/home/hornik/tmp/scratch/RtmpHYbyNW/nz4yC8"
     Using cached copy of .inputObjects event in child6 module.
     Using memoised copy of .inputObjects event in child6 module
     Using memoised copy of .inputObjects event in child6 module
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 452 | SKIPPED: 10 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: check all examples (@test-examples.R#11)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘test-all.R’ [292s/368s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     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
    
     [1] "/tmp/Rtmpqbaa_0/DWa3LC"
     [1] "/tmp/Rtmpqbaa_0/DWa3LC"
     [1] "/tmp/Rtmpqbaa_0/DWa3LC"
     [1] "/tmp/Rtmpqbaa_0/DWa3LC"
     Using cached copy of .inputObjects event in test module.
     ── 1. Error: check all examples (@test-examples.R#11) ─────────────────────────
     cannot open the connection
     1: test_examples(path = "../../man") at testthat/test-examples.R:11
     2: test_examples_source(path) %||% test_examples_installed(env_test$package)
     3: test_examples_installed(env_test$package)
     4: lapply(Rd, test_rd)
     5: FUN(X[[i]], ...)
     6: test_example(attr(rd, "Rdfile"))
     7: tools::Rd2ex(path, ex_path)
     8: prepare_Rd(Rd, defines = defines, stages = stages, ...)
     9: eval(substitute(parse_Rd(f, encoding = enc, fragment = frag, ...), list(f = Rd, enc = encoding,
     frag = fragment)))
     10: eval(substitute(parse_Rd(f, encoding = enc, fragment = frag, ...), list(f = Rd, enc = encoding,
     frag = fragment)))
     11: parse_Rd("/tmp/RtmpAAayZN/R.INSTALL4f9b12334d4b/SpaDES.core/man/Copy.Rd", encoding = "unknown",
     fragment = FALSE, ...)
     12: readLines(file, warn = FALSE)
     13: file(con, "r")
    
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/Oaxx2G"
     [1] "/tmp/Rtmpqbaa_0/nz4yC8"
     [1] "/tmp/Rtmpqbaa_0/nz4yC8"
     Using cached copy of .inputObjects event in child6 module.
     Using memoised copy of .inputObjects event in child6 module
     Using memoised copy of .inputObjects event in child6 module
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 458 | SKIPPED: 9 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: check all examples (@test-examples.R#11)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.5
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(
     reproducible.cachePath = '/tmp/Rtmp3VaOW3/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp39ay8N/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp39ay8N/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Quitting from lines 376-382 (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
    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
    
    Setting:
     options(
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpVIaq05/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp39ay8N/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp39ay8N/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    --- finished re-building ‘iii-cache.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.5
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
    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(
     reproducible.cachePath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmp8KUCdS/reproducible/cache'
     spades.inputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpRT9IDE/SpaDES/inputs'
     spades.outputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpRT9IDE/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'
     )
    Quitting from lines 376-382 (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
    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
    
    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(
     reproducible.cachePath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmp8KUCdS/reproducible/cache'
     spades.inputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpRT9IDE/SpaDES/inputs'
     spades.outputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpRT9IDE/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’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2.5
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpJ09Udo/reproducible/cache'
     spades.inputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpsLoOb1/SpaDES/inputs'
     spades.outputPath = '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpsLoOb1/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'
     )
    Quitting from lines 376-382 (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: OK: 12

Additional issues

rcnst