prepare for CRAN

[fdschneider]

Cleaning the package up for CRAN will require quite some work. Check produces plenty of warnings, mostly related with ASCII encoding, incomplete function definitions and documentation, generic method consistency, and some package dependencies.

Errors

• [x] * checking examples ... ERROR Running examples in 'traitdataform-Ex.R' failed The error occurred in: ...

  library('traitdataform') Error in library("traitdataform") : there is no package called 'traitdataform' Execution halted

Warnings

• [x] * checking S3 generic/method consistency ... WARNING print: function(x, ...) print.thesaurus: function(x) print: function(x, ...) print.trait: function(x) print: function(x, ...) print.traitdata: function(x) See section 'Generic functions and methods' in the 'Writing R Extensions' manual.
• [x] * checking Rd files ... WARNING amphibio.Rd: non-ASCII input and no declared encoding arthropodtraits.Rd: non-ASCII input and no declared encoding as.traitdata.Rd: non-ASCII input and no declared encoding heteroptera_raw.Rd: non-ASCII input and no declared encoding mammaldiet.Rd: non-ASCII input and no declared encoding read.service.Rd: non-ASCII input and no declared encoding problems found in 'amphibio.Rd', 'arthropodtraits.Rd', 'as.traitdata.Rd', 'heteroptera_raw.Rd', 'mammaldiet.Rd', 'read.service.Rd'
• [x] * checking for missing documentation entries ... WARNING Undocumented code objects: 'glossary' All user-level objects in a package should have documentation entries.
• [x] * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'as.trait' 'relationSource' 'source' Undocumented arguments in documentation object 'as.traitdata' 'id.vars' 'mutate' 'thesaurus' Undocumented arguments in documentation object 'standardize' 'warnings' Undocumented arguments in documentation object 'standardize.exploratories' 'plots' 'user' 'pswd' 'verbose' 'warnings' Undocumented arguments in documentation object 'standardize.taxonomy' '...' Undocumented arguments in documentation object 'standardize.traits' '...' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual.
• [x] * checking Rd contents ... WARNING Argument items with no description in Rd object 'as.trait': 'version' 'author' '...' Argument items with no description in Rd object 'as.traitdata': '...' Argument items with no description in Rd object 'standardize.traits': 'output'
• [x] * checking data for non-ASCII characters ... WARNING Warning: found non-ASCII strings
• [x] * checking data for ASCII and uncompressed saves ... OK WARNING 'qpdf' is needed for checks on size reduction of PDFs

Notes

• [x] * checking installed package size ... NOTE installed size is 34.0Mb sub-directories of 1Mb or more: Meta 8.0Mb R 3.0Mb data 8.0Mb doc 4.0Mb help 5.0Mb html 2.0Mb
• [x] * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT
• [x] * checking top-level files ... NOTE Non-standard files/directories found at top level: 'LICENSE.md' 'data_test' 'docs' 'draft'
• [x] * checking R code for possible problems ... NOTE get_gbif_taxonomy: no visible binding for global variable 'matchtype' get_gbif_taxonomy: no visible binding for global variable 'status' mutate.traitdata: no visible binding for global variable 'traitName' read.service: no visible global function definition for 'read.table' read.service.blocks: no visible global function definition for 'zip.unpack' read.service.blocks: no visible binding for global variable 'read.table' standardize.exploratories: no visible binding for global variable 'Landuse' standardize.exploratories: no visible binding for global variable 'Plot_ID' standardize.traits: no visible binding for global variable 'traitNameStd' Undefined global functions or variables: Landuse Plot_ID matchtype read.table status traitName traitNameStd zip.unpack Consider adding importFrom("utils", "read.table", "zip.unpack") to your NAMESPACE file.
• [x] * checking Rd line widths ... NOTE Rd file 'as.thesaurus.Rd': \examples lines wider than 100 characters: traitDescription = c("body length in mm", "length of antenna in mm", "length of metafemur in mm", "eye width in mm"), traits1 <- as.thesaurus(read.csv("https://raw.githubusercontent.com/EcologicalTraitData/TraitDataList/master/traitdatastandard_traitlis ... [TRUNCATED] Rd file 'cast.traitdata.Rd': \examples lines wider than 100 characters: traits = c("Body_Size", "Dispersal_ability", "Feeding_guild","Feeding_guild_short", "Feeding_mode", "Feeding_s ... [TRUNCATED] metadata = list(license = "http://creativecommons.org/publicdomain/zero/1.0/") Rd file 'get_gbif_taxonomy.Rd': \examples lines wider than 100 characters: get_gbif_taxonomy(c("Chorthippus albomarginatus", "Chorthippus apricarius", "Chorthippus biguttulus", "Chorthippus dorsatus", "Chorthip ... [TRUNCATED] Rd file 'mutate.traitdata.Rd': \examples lines wider than 100 characters: traits = c("Body_Size", "Dispersal_ability", "Feeding_guild","Feeding_guild_short", "Feeding_mode", "Feeding_s ... [TRUNCATED] metadata = list(license = "http://creativecommons.org/publicdomain/zero/1.0/") Rd file 'rbind.traitdata.Rd': \examples lines wider than 100 characters: dataset2 <- mutate.traitdata(dataset2, antenna_length = Antenna_Seg1 + Antenna_Seg2 + Antenna_Seg3 + Antenna_Seg4 + Antenna_Seg3 ) Rd file 'standardize.traits.Rd': \examples lines wider than 100 characters: dataset2 <- mutate.traitdata(dataset2, antenna_length = Antenna_Seg1 + Antenna_Seg2 + Antenna_Seg3 + Antenna_Seg4 + Antenna_Seg3 ) These lines will be truncated in the PDF manual.

[fdschneider]

v0.3.0 produced no errors and warnings on Windows. Now also implementing TRAVIS CI build testing for Linux. Take this as starting point for CRAN submission and will have all additional tasks as separate Issues.