ALA4R - Atlas of Living Australia (ALA) data and resources in R - check results
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ALA4R

About ALA4R
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Package R docs

Version: 1.01
Result: ERROR
Check time: 2018-01-24 13:57
* using log directory ''
* using R Under development (unstable) (2018-01-24 r74156)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'ALA4R/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ALA4R' version '1.01'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialized R objects in the sources ... OK
* checking whether package 'ALA4R' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'data.table' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_assertions: no visible global function definition for 'na.omit'
intersect_points: no visible global function definition for 'URLencode'
intersect_points: no visible global function definition for 'read.csv'
occurrences: no visible global function definition for
'installed.packages'
occurrences: no visible global function definition for 'unzip'
occurrences: no visible global function definition for 'fread'
occurrences: no visible global function definition for 'setnames'
occurrences: no visible global function definition for 'read.table'
occurrences_plot: no visible global function definition for 'data'
occurrences_plot: no visible binding for global variable 'aus'
occurrences_plot : tplot: no visible global function definition for
'image'
occurrences_plot : tplot: no visible binding for global variable 'aus'
occurrences_plot : tplot: no visible global function definition for
'title'
occurrences_plot : tplot: no visible global function definition for
'points'
occurrences_plot : tplot: no visible global function definition for
'legend'
occurrences_plot : tplot: no visible global function definition for
'rainbow'
occurrences_plot: no visible global function definition for 'pdf'
occurrences_plot : : no visible global function definition
for 'dev.off'
occurrences_plot: no visible global function definition for 'dev.off'
sites_by_species: no visible global function definition for 'URLencode'
sites_by_species: no visible global function definition for 'read.csv'
species_info: no visible global function definition for 'URLencode'
specieslist: no visible global function definition for 'read.table'
taxinfo_download: no visible global function definition for
'installed.packages'
taxinfo_download: no visible global function definition for 'fread'
taxinfo_download: no visible global function definition for 'setnames'
taxinfo_download: no visible global function definition for
'read.table'
unique.occurrences: no visible global function definition for
'aggregate'
Undefined global functions or variables:
URLencode aggregate aus data dev.off fread image installed.packages
legend na.omit pdf points rainbow read.csv read.table setnames title
unzip
Consider adding
importFrom("grDevices", "dev.off", "pdf", "rainbow")
importFrom("graphics", "image", "legend", "points", "title")
importFrom("stats", "aggregate", "na.omit")
importFrom("utils", "URLencode", "data", "installed.packages",
"read.csv", "read.table", "unzip")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'ALA4R/R/occurrences_plot.R':
data(aus)
See section 'Good practice' in '?data'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'intersect_points.Rd':
\examples lines wider than 100 characters:
# equivalent direct web service call: http://spatial.ala.org.au/ws/intersect/cl22,cl23,el773/-23.1/149.1

Rd file 'occurrences.Rd':
\examples lines wider than 100 characters:
x=occurrences(taxon="data_resource_uid:dr356",record_count_only=TRUE) ## count of records from this data provider
x=occurrences(taxon="data_resource_uid:dr356",download_reason_id=10) ## download records, with standard fields
x=occurrences(taxon="data_resource_uid:dr356",download_reason_id=10,fields=ala_fields("occurrence")$name) ## download records, with all ... [TRUNCATED]
x=occurrences(taxon="macropus",fields=c("longitude","latitude","common_name","taxon_name","el807"),download_reason_id=10) ## download r ... [TRUNCATED]
x=occurrences(taxon="macropus",wkt="POLYGON((145 -37,150 -37,150 -30,145 -30,145 -37))",download_reason_id=10,qa="none") ## download re ... [TRUNCATED]
# equivalent direct webservice call: http://biocache.ala.org.au/ws/occurrences/index/download?reasonTypeId=10&q=Alaba%20vibex&fields=la ... [TRUNCATED]
occurrences(taxon="Eucalyptus gunnii",fields=c("latitude","longitude"),qa="none",fq="basis_of_record:LivingSpecimen",download_reason_id ... [TRUNCATED]
# equivalent direct webservice call: http://biocache.ala.org.au/ws/occurrences/index/download?reasonTypeId=10&q=Eucalyptus%20gunnii&fie ... [TRUNCATED]

Rd file 'search_names.Rd':
\examples lines wider than 100 characters:
s1=search_names(c("Grevillea humilis","Grevillea humilis subsp. maritima","Macropus","Thisisnot aname"))
s2=search_names(c("Grevillea humilis","Grevillea humilis subsp. maritima","Macropus","Thisisnot aname"),guids_only=TRUE)
sv=search_names("Grevillea",vernacular=TRUE) ## should return the species Grevillea banksii, because it has the common name ``Grevillea ... [TRUNCATED]

Rd file 'sites_by_species.Rd':
\examples lines wider than 100 characters:
ss=sites_by_species(taxon='genus:Eucalyptus',wkt='POLYGON((144 -43,148 -43,148 -40,144 -40,144 -43))',gridsize=0.1,verbose=TRUE)
# equivalent direct webservice call: POST http://spatial.ala.org.au/alaspatial/ws/sitesbyspecies?speciesq=genus:Eucalyptus&qname=data&a ... [TRUNCATED]

Rd file 'specieslist.Rd':
\examples lines wider than 100 characters:
x=specieslist(wkt="POLYGON((147.62 -42.83,147.60 -42.86,147.65 -42.87,147.70 -42.86,147.62 -42.83))",fq="rank:species")

Rd file 'taxinfo_download.Rd':
\examples lines wider than 100 characters:
x=taxinfo_download("family:Fabaceae",fields=c("guid","parentGuid","kingdom","phylum","class","bioOrder","family","genus","nameComplete" ... [TRUNCATED]
## note that requesting "nameComplete" gives the scientific name but requesting "scientificName" will not --- bug to be fixed in ALA's ... [TRUNCATED]
# equivalent direct URL: http://bie.ala.org.au/ws/download?fields=guid,parentGuid,kingdom,phylum,class,bioOrder,family,genus,nameComple ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
WARNING
'qpdf' is needed for checks on size reduction of PDFs
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
'ALA4R.html'
* checking examples ... ERROR
Running examples in 'ALA4R-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: occurrences_s3
> ### Title: Summarize, filter and subset occurrence data
> ### Aliases: occurrences_s3 subset.occurrences summary.occurrences
> ### unique.occurrences
>
> ### ** Examples
>
> #download some observations
> x=occurrences(taxon="Amblyornis newtonianus",download_reason_id=10)
Loading required package: data.table
Please use (fixed|coll|regex)(x, ignore_case = TRUE) instead of ignore.case(x)
Please use (fixed|coll|regex)(x, ignore_case = TRUE) instead of ignore.case(x)
>
> #summarize the occurrences
> summary(x)
number of observation records: 1511
number of assertions listed: 18 -- ones with flagged issues are listed below
invalidCollectionDate: 110 records
incompleteCollectionDate: 150 records
firstOfCentury: 8 records
detectedOutlier: 4 records -- considered fatal
uncertaintyRangeMismatch: 17 records
firstOfYear: 39 records
altitudeInFeet: 2 records
geodeticDatumAssumedWgs84: 711 records
decimalLatLongConverted: 5 records
unrecognisedOccurrenceStatus: 1 records
coordinatePrecisionMismatch: 55 records
countryInferredByCoordinates: 481 records
assumedPresentOccurrenceStatus: 687 records
unrecognizedGeodeticDatum: 105 records
inferredDuplicateRecord: 101 records
stateCoordinateMismatch: 1 records
habitatMismatch: 14 records -- considered fatal
firstOfMonth: 96 records
>
> #keep spatially unique data at 0.01 degrees (latitude and longitude)
> tt = unique(x,spatial=0.01)
Error in `$<-.data.frame`(`*tmp*`, latitude, value = numeric(0)) :
replacement has 0 rows, data has 1511
Calls: unique -> unique.occurrences -> $<- -> $<-.data.frame
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
'/00check.log'
for details.


Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log