jarioksa
commented
6 years ago Reasons seem to be 1 ERROR, 4 WARNINGs, 1 NOTE. The greatest single problem seems to be that there is no function singleSppSitePair. After this function is added to the package, it is possible to proceed to the next stage of testing.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 1.1Mb
extdata 3.0Mb
* checking Rd metadata ... WARNING
Rd files with duplicated name 'gdm.varImp':
‘gd.varImp.Rd’ ‘gdm.varImp.Rd’
Rd files with duplicated alias 'gdm.varImp':
‘gd.varImp.Rd’ ‘gdm.varImp.Rd’
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'singleSppSitePair' but not in code:
singleSppSitePair
Codoc mismatches from documentation object 'gdm.varImp':
gdm.varImp
Code: function(spTable, geo, splines = NULL, knots = NULL,
fullModelOnly = FALSE, nPerm = 50, parallel = FALSE,
cores = 2, sampleSites = 1, sampleSitePairs = 1,
outFile = NULL)
Docs: function(spTable, geo, splines = NULL, knots = NULL,
fullModelOnly = FALSE, nPerm = 100, parallel = FALSE,
cores = 2)
Argument names in code not in docs:
sampleSites sampleSitePairs outFile
Mismatches in argument default values:
Name: 'nPerm' Code: 50 Docs: 100
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
gdm.RData 463Kb 274Kb xz
* checking examples ... ERROR
Running examples in ‘gdm-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: singleSppSitePair
> ### Title: Converts Common Biological (Response) and Environmental
> ### (Predictor) Data Formats to a GDM Site-Pair Table for a Single
> ### Species
> ### Aliases: singleSppSitePair
> ### Keywords: gdm
>
> ### ** Examples
>
>
> ##table data, species and environmental
> load(system.file("./data/gdm.RData", package="gdm"))
> sppData <- gdmExpData[c(1,2,13,14)]
> envTab <- gdmExpData[c(2:ncol(gdmExpData))]
>
> ##environmental raster data
> ##commented out to reduce example run time
> #rastFile <- system.file("./extdata/stackedVars.grd", package="gdm")
> #envRast <- stack(rastFile)
>
> #########table type 1
> ##site-species table without coordinates
> testData1a <- reshape2::dcast(sppData, site~species)
Using Long as value column: use value.var to override.
Aggregation function missing: defaulting to length
> ##site-species table with coordinates
> coords <- unique(sppData[2:ncol(sppData)])
> testData1b <- merge(testData1a, coords, by="site")
> ##site-species, table-table
> exFormat1a <- singleSppSitePair(testData1a, 1, siteColumn="site", XColumn="Long", YColumn="Lat",
+ sppID="spp258", predData=envTab)
Error in singleSppSitePair(testData1a, 1, siteColumn = "site", XColumn = "Long", :
could not find function "singleSppSitePair"
Execution haltedAnd one NOTE told that the package was archived due to these problems.
I'm sure you're aware of this, but CRAN doesn't allow installing the GDM package anymore. It'd be nice if you updated the package so that it continues to be supported.