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* using log directory ‘/XYZ/ArvadosR.Rcheck’
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* using R version 4.2.1 (2022-06-23)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* using session charset: UTF-8
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* using option ‘--no-build-vignettes’
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* checking for file ‘ArvadosR/DESCRIPTION’ ... OK
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* checking extension type ... Package
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* this is package ‘ArvadosR’ version ‘2.5.0’
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* package encoding: UTF-8
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* checking package namespace information ... OK
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* checking package dependencies ... OK
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* checking if this is a source package ... OK
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* checking if there is a namespace ... OK
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|
* checking for executable files ... OK
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* checking for hidden files and directories ... OK
|
|
* checking for portable file names ... OK
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|
* checking for sufficient/correct file permissions ... OK
|
|
* checking whether package ‘ArvadosR’ can be installed ... OK
|
|
* checking installed package size ... OK
|
|
* checking package directory ... OK
|
|
* checking DESCRIPTION meta-information ... NOTE
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Malformed Description field: should contain one or more complete sentences.
|
|
Non-standard license specification:
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|
Apache-2.0
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|
Standardizable: FALSE
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* 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
|
|
Namespaces in Imports field not imported from:
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|
‘R6’ ‘XML’ ‘curl’ ‘jsonlite’
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|
All declared Imports should be used.
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|
* checking S3 generic/method consistency ... OK
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|
* checking replacement functions ... OK
|
|
* checking foreign function calls ... OK
|
|
* checking R code for possible problems ... NOTE
|
|
File ‘ArvadosR/R/zzz.R’:
|
|
.onLoad calls:
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|
print(paste0("Minimum R version required to run ", pkgName, " is ", minAllowedRVersion, ". Your current version is ", toString(currentRVersion), ". Please update R and try again."))
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|
|
|
Package startup functions should use ‘packageStartupMessage’ to
|
|
generate messages.
|
|
See section ‘Good practice’ in '?.onAttach'.
|
|
* checking Rd files ... OK
|
|
* checking Rd metadata ... OK
|
|
* checking Rd cross-references ... WARNING
|
|
Missing link or links in documentation object 'ArvadosR.Rd':
|
|
‘https://github.com/arvados/arvados/blob/main/README.md’
|
|
‘https://github.com/arvados/arvados/tree/main/sdk/R’
|
|
|
|
Missing link or links in documentation object 'Collection.Rd':
|
|
‘https://github.com/arvados/arvados/tree/main/sdk/R’
|
|
|
|
See section 'Cross-references' in the 'Writing R Extensions' manual.
|
|
* checking for missing documentation entries ... WARNING
|
|
Undocumented code objects:
|
|
‘generateAPI’
|
|
All user-level objects in a package should have documentation entries.
|
|
See chapter ‘Writing R documentation files’ in the ‘Writing R
|
|
Extensions’ manual.
|
|
* checking for code/documentation mismatches ... OK
|
|
* checking Rd \usage sections ... OK
|
|
* checking Rd contents ... OK
|
|
* checking for unstated dependencies in examples ... OK
|
|
* checking examples ... ERROR
|
|
Running examples in ‘ArvadosR-Ex.R’ failed
|
|
The error most likely occurred in:
|
|
|
|
> ### Name: Arvados
|
|
> ### Title: R6 Class Representing a Arvados
|
|
> ### Aliases: Arvados
|
|
>
|
|
> ### ** Examples
|
|
>
|
|
>
|
|
> ## ------------------------------------------------
|
|
> ## Method `Arvados$new`
|
|
> ## ------------------------------------------------
|
|
>
|
|
> arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)
|
|
>
|
|
> ## ------------------------------------------------
|
|
> ## Method `Arvados$project_exist`
|
|
> ## ------------------------------------------------
|
|
>
|
|
> arv$project_exist(uuid = projectUUID)
|
|
Error in filters[[length(filters) + 1]] <- list("group_class", "=", "project") :
|
|
object 'projectUUID' not found
|
|
Calls: <Anonymous> -> <Anonymous>
|
|
Execution halted
|
|
* checking for unstated dependencies in ‘tests’ ... OK
|
|
* checking tests ...
|
|
OK
|
|
* checking PDF version of manual ... OK
|
|
* DONE
|
|
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
|