Last updated on 2024-06-12 06:58:15 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 51.41 | 600.77 | 652.18 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 37.16 | 435.56 | 472.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 810.71 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 787.47 | NOTE | |||
| r-devel-windows-x86_64 | 1.1.1 | 36.00 | 398.00 | 434.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 37.96 | 563.89 | 601.85 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 46.69 | 579.42 | 626.11 | OK | |
| r-release-macos-arm64 | 1.1.1 | 208.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.1 | 421.00 | OK | |||
| r-release-windows-x86_64 | 1.1.1 | 35.00 | 417.00 | 452.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 251.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.1.1 | 492.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.1 | 51.00 | 514.00 | 565.00 | OK |
Version: 1.1.1
Check: data for non-ASCII characters
Result: NOTE
Note: found 107 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-formattedCombiner.R:61:1'): (code run outside of `test_that()`) ──
Error in `file(.)`: invalid 'description' argument
Backtrace:
▆
1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
2. │ └─... %>% xml2::read_xml()
3. ├─xml2::read_xml(.)
4. └─base::file(.)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 238 ]
Error: Test failures
Execution halted
Warning message:
Connection is garbage-collected, use dbDisconnect() to avoid this.
Flavor: r-release-macos-arm64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-formattedCombiner.R:61:1'): (code run outside of `test_that()`) ──
Error in `file(.)`: invalid 'description' argument
Backtrace:
▆
1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
2. │ └─... %>% xml2::read_xml()
3. ├─xml2::read_xml(.)
4. └─base::file(.)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 238 ]
Error: Test failures
Execution halted
Warning message:
Connection is garbage-collected, use dbDisconnect() to avoid this.
Flavor: r-oldrel-macos-arm64
Version: 1.1.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘BeeBDC_main.Rmd’
...
> rm(testChecklist)
> check_space <- BeeBDC::countryOutlieRs(checklist = checklistFile,
+ data = check_space, keepAdjacentCountry = TRUE, pointBuffer = 0.05,
+ .... [TRUNCATED]
When sourcing ‘BeeBDC_main.R’:
Error: object 'checklistFile' not found
Execution halted
‘BeeBDC_main.Rmd’ using ‘UTF-8’... failed
‘basic_workflow.Rmd’ using ‘UTF-8’... [11s/13s] OK
Flavor: r-oldrel-macos-arm64
Version: 1.1.1
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
--- re-building ‘BeeBDC_main.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
You changed the working directory to /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpAuQD10/Data_acquisition_workflow (probably via setwd()). It will be restored to /Volumes/Builds/packages/big-sur-arm64/results/4.3/BeeBDC.Rcheck/vign_test/BeeBDC/vignettes. See the Note section in ?knitr::knit
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.0'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Only keep a subset of columns from bees3sp.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: bees3sp
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.4'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:6:1: unexpected string constant
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Keep all plus some at the bottom..HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: "Event"
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.5a'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Create a Tibble of common issues in country names and their replacements.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: commonProblems
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.5b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:7:1: unexpected symbol
6: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# How many rows to process at a time.HaHaHa_EnD_TiDy_IdEnTiFiEr")
7: stepSize
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.6'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:6:1: unexpected symbol
5:
6: data
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.7'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# bdc_coordinates_transposed inputs.HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: data
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.11'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# DON'T flag if in the following dataSource(s).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: excludeDataSource
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.13a'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:6:1: unexpected symbol
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# These are the columns that will be kept along with the flags.HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: idColumns
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '3.13b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Don't filter these columns (or NULL).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '4.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:1:54: unexpected SPECIAL
1: database <- BeeBDC :: harmoniseR ( path = DataPath , %<08>%
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:7:20: unexpected SPECIAL
6: species = "scientificName" ,
7: countries = NULL , %<08>%
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The minimum number of repeats needed to find a sequence in for flagging.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: minRepeats
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.3iv'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Select the columns of interest.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: dplyr
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.5ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:8:1: unexpected symbol
7:
8: scale
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.6ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:2:124: unexpected SPECIAL
1: check_space %<08>> %
2: dplyr :: filter ( .summary == FALSE ) %<08>> % %<08>%
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '6.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Years above this are removed (from the recovered dates only).HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: maxYear
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '6.4'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Don't filter these columns (or NULL).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '7.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# options are 'ID','collectionInfo', or 'both'.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: duplicatedBy
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '8.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:6:1: unexpected symbol
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Remove the filtering columns?.HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: removeFilterColumns
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '9.1iv'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The duplicate data from the dupeSummary function output .HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: dupeData
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '9.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The outPath to save the plot as.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: outPath
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '9.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Colours in order of pass (TRUE), fail (FALSE), and NA.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: flagColours
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '9.4b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# occurrence data.HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: data
^
Could not fetch https://photos.smugmug.com/photos/i-Xt3tN8L/0/X5/i-Xt3tN8L-X5.jpg
HttpExceptionRequest Request {
host = "photos.smugmug.com"
port = 443
secure = True
requestHeaders = []
path = "/photos/i-Xt3tN8L/0/X5/i-Xt3tN8L-X5.jpg"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
}
(ConnectionFailure Network.Socket.getAddrInfo (called with preferred socket type/protocol: AddrInfo {addrFlags = [AI_ADDRCONFIG], addrFamily = AF_UNSPEC, addrSocketType = Stream, addrProtocol = 0, addrAddress = <assumed to be undefined>, addrCanonName = <assumed to be undefined>}, host name: Just "photos.smugmug.com", service name: Just "443"): does not exist (nodename nor servname provided, or not known))
Error: processing vignette 'BeeBDC_main.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘BeeBDC_main.Rmd’
--- re-building ‘basic_workflow.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
You changed the working directory to /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpfzfKGN/Data_acquisition_workflow (probably via setwd()). It will be restored to /Volumes/Builds/packages/big-sur-arm64/results/4.3/BeeBDC.Rcheck/vign_test/BeeBDC/vignettes. See the Note section in ?knitr::knit
Warning in eng_r(options) :
Failed to tidy R code in chunk '4.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Choose the columns to NOT filter (or NULL to filter all columns).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '4.2'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:8:1: unexpected symbol
7: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# 10 km here.HaHaHa_EnD_TiDy_IdEnTiFiEr")
8: threshold
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '4.2b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Select the input dataset to filter.HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: data
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.1iii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The duplicate data from the dupeSummary function output .HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: dupeData
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.2'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The outPath to save the plot as.HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: outPath
^
Warning in eng_r(options) :
Failed to tidy R code in chunk '5.3b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:6:1: unexpected symbol
5:
6: data
^
--- finished re-building ‘basic_workflow.Rmd’
SUMMARY: processing the following file failed:
‘BeeBDC_main.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64