Add ecoregionalization workflow

[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.

[github-actions]

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:

          • 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:

          • 0

          Standard Error:

          • 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 (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
            Warning message:
            Failed to locate timezone database 
            

          Standard Output:

          • null device 
                      1 
            

          Traceback:

          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	"?"
            k	"3"
            metric	"manhattan"
            sample	"10"

    • Step 5: EcoMap:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • 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:

          • 0

          Standard Error:

          • 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:

          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	"?"

  • Other invocation details

    • history_id

      • c93240b43ff26df7

    • history_state

      • ok

    • invocation_id

      • c00e873e829f1945

    • invocation_state

      • scheduled

    • workflow_id

      • c93240b43ff26df7

[github-actions]

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:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/74e966baa5fd/ecoregion_clara_cluster/cluster_ceamarc.R' '/tmp/tmpqa1z4ypj/files/e/e/6/dataset_ee6ea192-133e-4be8-922a-a2e5a1fd3297.dat' '/tmp/tmpqa1z4ypj/files/2/8/0/dataset_28038a97-829b-4617-adff-35f5813d17ea.dat' '/tmp/tmpqa1z4ypj/files/8/5/1/dataset_85151ebe-cbcf-4f4b-af84-f1719f143efa.dat' '3' 'manhattan' '10' '/tmp/tmpqa1z4ypj/job_working_directory/000/7/outputs/dataset_35ea569e-e06d-4b00-b7bf-0e703c814289.dat' '/tmp/tmpqa1z4ypj/job_working_directory/000/7/outputs/dataset_04d28578-f036-4a97-bf75-5e220ae9399e.dat' '/tmp/tmpqa1z4ypj/job_working_directory/000/7/outputs/dataset_c1244d7a-20fe-45d4-9711-b3bee6af9ea1.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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 (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
            Warning message:
            Failed to locate timezone database 
            

          Standard Output:

          • null device 
                      1 
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3341bd909b7e11efaec265debfc7e83c"
            chromInfo	"/tmp/tmpqa1z4ypj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            k	"3"
            metric	"manhattan"
            sample	"10"

    • Step 5: EcoMap:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/45784ebada45/ecoregion_eco_map/crea_carte_G.R' '/tmp/tmpqa1z4ypj/files/0/4/d/dataset_04d28578-f036-4a97-bf75-5e220ae9399e.dat' '/tmp/tmpqa1z4ypj/job_working_directory/000/8/outputs/dataset_174d7184-a996-432c-aabe-ac4ec237406b.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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/tmpqa1z4ypj/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:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3341bd909b7e11efaec265debfc7e83c"
            chromInfo	"/tmp/tmpqa1z4ypj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • 13d352766ed0eb6c

    • history_state

      • ok

    • invocation_id

      • 3cf527b13b98bed6

    • invocation_state

      • scheduled

    • workflow_id

      • 13d352766ed0eb6c

[github-actions]

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:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/74e966baa5fd/ecoregion_clara_cluster/cluster_ceamarc.R' '/tmp/tmpvw7aleqm/files/1/e/3/dataset_1e36a880-0639-49d9-9b3d-73307ce95632.dat' '/tmp/tmpvw7aleqm/files/6/0/e/dataset_60e3c969-7fe7-477a-8d05-58ba92ca3b3f.dat' '/tmp/tmpvw7aleqm/files/1/5/c/dataset_15c6eed8-b0c0-4281-ae32-977a30deffef.dat' '3' 'manhattan' '10' '/tmp/tmpvw7aleqm/job_working_directory/000/7/outputs/dataset_53250811-3eca-4697-8e8b-f2f864ff5ccd.dat' '/tmp/tmpvw7aleqm/job_working_directory/000/7/outputs/dataset_e9e7b1a6-b64e-4536-ac14-a816c110d859.dat' '/tmp/tmpvw7aleqm/job_working_directory/000/7/outputs/dataset_3ef9d182-8e19-41b8-a258-feb548b5b958.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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 (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
            Warning message:
            Failed to locate timezone database 
            

          Standard Output:

          • null device 
                      1 
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"31b582f49b8311ef9dcb51c96a57802e"
            chromInfo	"/tmp/tmpvw7aleqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            k	"3"
            metric	"manhattan"
            sample	"10"

    • Step 5: EcoMap:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/45784ebada45/ecoregion_eco_map/crea_carte_G.R' '/tmp/tmpvw7aleqm/files/e/9/e/dataset_e9e7b1a6-b64e-4536-ac14-a816c110d859.dat' '/tmp/tmpvw7aleqm/job_working_directory/000/8/outputs/dataset_206bdb9e-8fb7-4307-8f55-33a076d99b18.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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/tmpvw7aleqm/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:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"31b582f49b8311ef9dcb51c96a57802e"
            chromInfo	"/tmp/tmpvw7aleqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • ef5b412368c56220

    • history_state

      • ok

    • invocation_id

      • 19bc32e94f717011

    • invocation_state

      • scheduled

    • workflow_id

      • ef5b412368c56220

[github-actions]

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:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/74e966baa5fd/ecoregion_clara_cluster/cluster_ceamarc.R' '/tmp/tmpb6lcm9ms/files/5/9/f/dataset_59f4e296-1885-4e6f-90ca-a28edf0feb17.dat' '/tmp/tmpb6lcm9ms/files/7/c/4/dataset_7c4a2397-0923-4f9d-9d64-04d15b392453.dat' '/tmp/tmpb6lcm9ms/files/8/f/1/dataset_8f1578dc-24d3-4a85-96f1-ab638f15b8a2.dat' '3' 'manhattan' '10' '/tmp/tmpb6lcm9ms/job_working_directory/000/7/outputs/dataset_98147e7d-349a-497d-a02c-e2a5c6c0c992.dat' '/tmp/tmpb6lcm9ms/job_working_directory/000/7/outputs/dataset_2e02add5-f2d5-4b17-8025-63690426fbae.dat' '/tmp/tmpb6lcm9ms/job_working_directory/000/7/outputs/dataset_358a86ff-587b-45a3-a58d-99d8d7ef8421.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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 (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
            Warning message:
            Failed to locate timezone database 
            

          Standard Output:

          • null device 
                      1 
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"6a6b126c9b8311ef9c75c79efeb73420"
            chromInfo	"/tmp/tmpb6lcm9ms/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            k	"3"
            metric	"manhattan"
            sample	"10"

    • Step 5: EcoMap:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/45784ebada45/ecoregion_eco_map/crea_carte_G.R' '/tmp/tmpb6lcm9ms/files/2/e/0/dataset_2e02add5-f2d5-4b17-8025-63690426fbae.dat' '/tmp/tmpb6lcm9ms/job_working_directory/000/8/outputs/dataset_5af6b517-7400-4b52-b272-2123416418eb.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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/tmpb6lcm9ms/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:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"6a6b126c9b8311ef9c75c79efeb73420"
            chromInfo	"/tmp/tmpb6lcm9ms/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • fe18829da219baee

    • history_state

      • ok

    • invocation_id

      • 4ab662782ea40c29

    • invocation_state

      • scheduled

    • workflow_id

      • fe18829da219baee

[github-actions]

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:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/74e966baa5fd/ecoregion_clara_cluster/cluster_ceamarc.R' '/tmp/tmpy566nmnv/files/d/9/b/dataset_d9b3c3a9-98db-40cf-8c5c-8238fd82eb02.dat' '/tmp/tmpy566nmnv/files/0/f/e/dataset_0fe755fe-1ba8-445a-95fa-ec6910b6852d.dat' '/tmp/tmpy566nmnv/files/5/e/9/dataset_5e96d7c3-8465-4a09-83b2-000dcad20a72.dat' '3' 'manhattan' '10' '/tmp/tmpy566nmnv/job_working_directory/000/7/outputs/dataset_7db47184-0aee-4f13-a9f0-aac3d72217ff.dat' '/tmp/tmpy566nmnv/job_working_directory/000/7/outputs/dataset_4494c7fa-9ca4-4cfb-b766-400c2e84df5e.dat' '/tmp/tmpy566nmnv/job_working_directory/000/7/outputs/dataset_76bf82f5-195b-4a75-828b-50cf2e524037.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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 (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
            Warning message:
            Failed to locate timezone database 
            

          Standard Output:

          • null device 
                      1 
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"493584169b8711ef80324303f61a569c"
            chromInfo	"/tmp/tmpy566nmnv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            k	"3"
            metric	"manhattan"
            sample	"10"

    • Step 5: EcoMap:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/45784ebada45/ecoregion_eco_map/crea_carte_G.R' '/tmp/tmpy566nmnv/files/4/4/9/dataset_4494c7fa-9ca4-4cfb-b766-400c2e84df5e.dat' '/tmp/tmpy566nmnv/job_working_directory/000/8/outputs/dataset_f037cfe4-6dc3-46f3-9c58-b1c22b0be204.dat'

          Exit Code:

          • 0

          Standard Error:

          • 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/tmpy566nmnv/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:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"493584169b8711ef80324303f61a569c"
            chromInfo	"/tmp/tmpy566nmnv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • 5f99cdd049445f09

    • history_state

      • ok

    • invocation_id

      • 901a853b486000ef

    • invocation_state

      • scheduled

    • workflow_id

      • 5f99cdd049445f09

[PaulineSGN]

Hi @galaxyproject/iwc it seems that the test is not passing because Planemo don't handle interactive tools yet. Let me know if I'm wrong. However, I think it's ready for review. Thanks a lot for your help.

[mvdbeek]

Hey @PaulineSGN, yes, that's right. I think we'll probably need to enable pause steps for workflows with ITs to really make sense, otherwise the IT will just start (and keep) running when the inputs are ready.