Last updated on 2025-05-17 08:49:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 34.62 | 507.96 | 542.58 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 23.90 | 367.71 | 391.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 299.20 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 300.65 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.0 | 42.00 | 444.00 | 486.00 | OK | |
| r-release-macos-arm64 | 1.2.0 | 217.00 | OK | |||
| r-release-windows-x86_64 | 1.2.0 | 47.00 | 472.00 | 519.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | 260.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.0 | 193.00 | ERROR |
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘spatialGE-Ex.R’ failed
The error most likely occurred in:
> ### Name: STlist
> ### Title: STlist: Creation of STlist objects for spatial transcriptomics
> ### analysis
> ### Aliases: STlist
>
> ### ** Examples
>
>
> # Using included melanoma example (Thrane et al.)
> # Download example data set from spatialGE_Data
> thrane_tmp = tempdir()
> unlink(thrane_tmp, recursive=TRUE)
> dir.create(thrane_tmp)
> lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
> download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'), mode='wb')
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Warning in download.file(lk, destfile = paste0(thrane_tmp, "/", "melanoma_thrane.zip"), :
URL 'https://media.githubusercontent.com/media/FridleyLab/spatialGE_Data/refs/heads/main/melanoma_thrane.zip?download=true': status was 'SSL peer certificate or SSH remote key was not OK'
Error in download.file(lk, destfile = paste0(thrane_tmp, "/", "melanoma_thrane.zip"), :
cannot open URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(spatialGE)
>
> test_check("spatialGE")
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-tests.R:9:1'): (code run outside of `test_that()`) ─────────────
Error in `download.file("https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download=",
destfile = paste0(thrane_tmp, "/", "melanoma_thrane.zip"),
mode = "wb")`: cannot open URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Backtrace:
▆
1. └─utils::download.file(...) at test-tests.R:9:1
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘basic_functions_vignette.Rmd’ using rmarkdown
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download='
Quitting from basic_functions_vignette.Rmd:75-83 [data_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download='
---
Backtrace:
▆
1. └─utils::download.file(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'basic_functions_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download='
--- failed re-building ‘basic_functions_vignette.Rmd’
SUMMARY: processing the following file failed:
‘basic_functions_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(spatialGE)
>
> test_check("spatialGE")
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-tests.R:9:1'): (code run outside of `test_that()`) ─────────────
Error in `download.file("https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download=",
destfile = paste0(thrane_tmp, "/", "melanoma_thrane.zip"),
mode = "wb")`: cannot open URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Backtrace:
▆
1. └─utils::download.file(...) at test-tests.R:9:1
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘spatialGE-Ex.R’ failed
The error most likely occurred in:
> ### Name: STlist
> ### Title: STlist: Creation of STlist objects for spatial transcriptomics
> ### analysis
> ### Aliases: STlist
>
> ### ** Examples
>
>
> # Using included melanoma example (Thrane et al.)
> # Download example data set from spatialGE_Data
> thrane_tmp = tempdir()
> unlink(thrane_tmp, recursive=TRUE)
> dir.create(thrane_tmp)
> lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
> download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'), mode='wb')
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Content type 'application/zip' length 3400344 bytes (3.2 MB)
==================================================
downloaded 3.2 MB
> zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
> unzip(zipfile=zip_tmp, exdir=thrane_tmp)
Warning in unzip(zipfile = zip_tmp, exdir = thrane_tmp) :
write error in extracting from zip file
> # Generate the file paths to be passed to the STlist function
> count_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+ full.names=TRUE, pattern='counts')
> coord_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+ full.names=TRUE, pattern='mapping')
> clin_file <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+ full.names=TRUE, pattern='clinical')
> # Create STlist
> library('spatialGE')
> melanoma <- STlist(rnacounts=count_files[c(1,3)],
+ spotcoords=coord_files[c(1,3)],
+ samples=clin_file) # Only first three samples
Error: Invalid argument
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(spatialGE)
>
> test_check("spatialGE")
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Content type 'application/zip' length 3400344 bytes (3.2 MB)
==================================================
downloaded 3.2 MB
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-tests.R:17:1'): (code run outside of `test_that()`) ────────────
Error: Invalid argument
Backtrace:
▆
1. └─spatialGE::STlist(...) at test-tests.R:17:1
2. └─readr::read_delim(...)
3. └─vroom::vroom(...)
4. └─vroom:::vroom_(...)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘basic_functions_vignette.Rmd’ using rmarkdown
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download='
Content type 'application/zip' length 119463578 bytes (113.9 MB)
============
downloaded 27.7 MB
Quitting from basic_functions_vignette.Rmd:75-83 [data_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! download from 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download=' failed
---
Backtrace:
▆
1. └─utils::download.file(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'basic_functions_vignette.Rmd' failed with diagnostics:
download from 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download=' failed
--- failed re-building ‘basic_functions_vignette.Rmd’
SUMMARY: processing the following file failed:
‘basic_functions_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64