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* using log directory ‘/XYZ/ArvadosR.Rcheck’
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2
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* using R version 4.2.1 (2022-06-23)
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3
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* using platform: x86_64-pc-linux-gnu (64-bit)
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4
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* using session charset: UTF-8
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5
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* using option ‘--no-build-vignettes’
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6
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* checking for file ‘ArvadosR/DESCRIPTION’ ... OK
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7
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* checking extension type ... Package
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8
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* this is package ‘ArvadosR’ version ‘2.5.0’
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9
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* package encoding: UTF-8
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10
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* checking package namespace information ... OK
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11
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* checking package dependencies ... OK
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12
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* checking if this is a source package ... OK
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13
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* checking if there is a namespace ... OK
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14
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* checking for executable files ... OK
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15
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* checking for hidden files and directories ... OK
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16
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* checking for portable file names ... OK
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17
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* checking for sufficient/correct file permissions ... OK
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18
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* checking whether package ‘ArvadosR’ can be installed ... OK
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19
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* checking installed package size ... OK
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20
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* checking package directory ... OK
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21
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* checking DESCRIPTION meta-information ... NOTE
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22
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Malformed Description field: should contain one or more complete sentences.
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23
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Non-standard license specification:
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24
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Apache-2.0
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25
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Standardizable: FALSE
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26
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* checking top-level files ... OK
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27
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* checking for left-over files ... OK
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28
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* checking index information ... OK
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29
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* checking package subdirectories ... OK
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30
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* checking R files for non-ASCII characters ... OK
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31
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* checking R files for syntax errors ... OK
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32
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* checking whether the package can be loaded ... OK
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33
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* checking whether the package can be loaded with stated dependencies ... OK
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34
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* checking whether the package can be unloaded cleanly ... OK
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35
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* checking whether the namespace can be loaded with stated dependencies ... OK
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36
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* checking whether the namespace can be unloaded cleanly ... OK
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37
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* checking loading without being on the library search path ... OK
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38
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* checking dependencies in R code ... NOTE
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39
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Namespaces in Imports field not imported from:
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40
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‘R6’ ‘XML’ ‘curl’ ‘jsonlite’
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41
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All declared Imports should be used.
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42
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* checking S3 generic/method consistency ... OK
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43
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* checking replacement functions ... OK
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44
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* checking foreign function calls ... OK
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45
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* checking R code for possible problems ... NOTE
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46
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File ‘ArvadosR/R/zzz.R’:
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47
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.onLoad calls:
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48
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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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49
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50
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Package startup functions should use ‘packageStartupMessage’ to
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51
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generate messages.
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52
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See section ‘Good practice’ in '?.onAttach'.
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53
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* checking Rd files ... OK
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54
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* checking Rd metadata ... OK
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55
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* checking Rd cross-references ... WARNING
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56
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Missing link or links in documentation object 'ArvadosR.Rd':
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57
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‘https://github.com/arvados/arvados/blob/main/README.md’
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58
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‘https://github.com/arvados/arvados/tree/main/sdk/R’
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59
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60
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Missing link or links in documentation object 'Collection.Rd':
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61
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‘https://github.com/arvados/arvados/tree/main/sdk/R’
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62
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63
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See section 'Cross-references' in the 'Writing R Extensions' manual.
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64
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* checking for missing documentation entries ... WARNING
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65
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Undocumented code objects:
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66
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‘generateAPI’
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67
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All user-level objects in a package should have documentation entries.
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68
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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69
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Extensions’ manual.
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70
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* checking for code/documentation mismatches ... OK
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71
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* checking Rd \usage sections ... OK
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72
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* checking Rd contents ... OK
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73
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* checking for unstated dependencies in examples ... OK
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74
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* checking examples ... ERROR
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75
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Running examples in ‘ArvadosR-Ex.R’ failed
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76
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The error most likely occurred in:
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77
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78
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> ### Name: Arvados
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79
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> ### Title: R6 Class Representing a Arvados
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80
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> ### Aliases: Arvados
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81
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>
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82
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> ### ** Examples
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83
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>
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84
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>
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85
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> ## ------------------------------------------------
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86
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> ## Method `Arvados$new`
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87
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> ## ------------------------------------------------
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88
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>
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89
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> arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)
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90
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>
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91
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> ## ------------------------------------------------
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92
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> ## Method `Arvados$project_exist`
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93
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> ## ------------------------------------------------
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94
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>
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95
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> arv$project_exist(uuid = projectUUID)
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96
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Error in filters[[length(filters) + 1]] <- list("group_class", "=", "project") :
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97
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object 'projectUUID' not found
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98
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Calls: <Anonymous> -> <Anonymous>
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99
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Execution halted
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100
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* checking for unstated dependencies in ‘tests’ ... OK
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101
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* checking tests ...
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102
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OK
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103
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* checking PDF version of manual ... OK
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104
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* DONE
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105
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Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
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