github-actions[bot]
commented
1 week ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 2 |
| Passed | 1 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
*❌ Ecoregionalization_workflow_Part_1.ga_0
**Execution Problem:**
* ```
Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: interactive_tool_jupyter_notebook (version 1.0.0)","err_code":0}
```
Passed Tests
*✅ Ecoregionalization_workflow_Part_2.ga_0
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: ceamarc_env.tabular**: * step_state: scheduled - **Step 2: Data_to_cluster.tabular**: * step_state: scheduled - **Step 3: Data.bio_table.tabular**: * step_state: scheduled - **Step 4: ClaraClust**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/74e966baa5fd/ecoregion_clara_cluster/cluster_ceamarc.R' '/tmp/tmp6t0u8ygq/files/e/4/0/dataset_e4041fa5-ac55-4668-83fe-0ba6ea746f92.dat' '/tmp/tmp6t0u8ygq/files/9/1/0/dataset_9104c7fb-9f3c-45b0-8f6a-2e6e158b8582.dat' '/tmp/tmp6t0u8ygq/files/5/9/5/dataset_595a4c5c-526f-41df-af99-c21aaf931b9f.dat' '3' 'manhattan' '10' '/tmp/tmp6t0u8ygq/job_working_directory/000/7/outputs/dataset_6128abc0-ba05-4b65-b8a7-a68fbeece9a0.dat' '/tmp/tmp6t0u8ygq/job_working_directory/000/7/outputs/dataset_00616d0c-9a51-4209-b767-b87f55fc7919.dat' '/tmp/tmp6t0u8ygq/job_working_directory/000/7/outputs/dataset_25fdea44-1a12-44bb-931c-28fd18de4490.dat' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ forcats 1.0.0 ✔ readr 2.1.4 ✔ ggplot2 3.4.4 ✔ stringr 1.5.0 ✔ lubridate 1.9.3 ✔ tibble 3.2.1 ✔ purrr 1.0.2 ✔ tidyr 1.3.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() ℹ Use the conflicted package ( - **Step 5: EcoMap**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/45784ebada45/ecoregion_eco_map/crea_carte_G.R' '/tmp/tmp6t0u8ygq/files/0/0/6/dataset_00616d0c-9a51-4209-b767-b87f55fc7919.dat' '/tmp/tmp6t0u8ygq/job_working_directory/000/8/outputs/dataset_57199261-ead8-4ab0-acff-97161e66493a.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Linking to GEOS 3.11.2, GDAL 3.7.0, PROJ 9.2.0; sf_use_s2() is TRUE
code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatOptions” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatOptions” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRaster” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRaster” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRasterCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRasterCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRasterStack” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatRasterStack” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatSRS” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatSRS” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
Breaking News: tmap 3.x is retiring. Please test v4, e.g. with
remotes::install_github('r-tmap/tmap')
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Map saved to /tmp/tmp6t0u8ygq/job_working_directory/000/8/working/ecoregions.png
Resolution: 2787.558 by 1582.03 pixels
Size: 9.291859 by 5.273434 inches (300 dpi)
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "164bfab29b7d11ef92eb33678372807c" ` |
| chromInfo | ` "/tmp/tmp6t0u8ygq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
</details>-
Other invocation details
- **history_id** * c93240b43ff26df7 - **history_state** * ok - **invocation_id** * c00e873e829f1945 - **invocation_state** * scheduled - **workflow_id** * c93240b43ff26df7
PaulineSGN
Hello, I would like to propose this workflow (in two parts) in connection with the GTN "Ecoregionalization workflow tutorial". Don't hesitate to correct this pull request or indicates me what to change if needed, it's my first pull request on this repository and I'm not fully familiar with iwc specification. Thank you.