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weecology / retriever

Quickly download, clean up, and install public datasets into a database management system
http://data-retriever.org
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Scripts not automatically downloading at installation #892

Closed davharris closed 7 years ago

davharris commented 7 years ago

While trying to reproduce Kristina's results, I downloaded the retriever with pip install. Next, I tried to download the vertnet data from within R using

rdataretriever::install("vertnet", "csv", data_dir = "data/")

I got the following:

The dataset vertnet isn’t currently available in the Retriever 
Run ’retriever ls to see a list of currently available datasets

Once I ran retriever ls, everything was fine. But it seems like this should be part of the default pip installation process, I think?

I'm on mac 10.11.6 "El Capitan" using retriever v2.0.0 and Anaconda Python 2.7.13

ethanwhite commented 7 years ago

Sorry for the delay @davharris. You're totally right, this should have been happening automatically since https://github.com/henrykironde/retriever/commit/5db19ee330b953e1f53fd7232ebff3662ea3996b. We'll dig into it and see what we can figure out.

ahhurlbert commented 7 years ago

Unsure if this is a related or separate issue. I just installed the latest retriever version:

$ pip install retriever --upgrade
Collecting retriever
  Downloading retriever-2.0.0-py2.py3-none-any.whl (159kB)
Requirement already up-to-date: xlrd in c:\anaconda2\lib\site-packages (from retriever)
Collecting future (from retriever)
  Downloading future-0.16.0.tar.gz (824kB)
Building wheels for collected packages: future
  Running setup.py bdist_wheel for future: started
  Running setup.py bdist_wheel for future: finished with status 'done'
  Stored in directory: C:\Users\hurlbert\AppData\Local\pip\Cache\wheels\c2\50\7c\0d83b4baac4f63ff7a765bd16390d2ab43c93587fac9d6017a
Successfully built future
Installing collected packages: future, retriever
  Found existing installation: future 0.15.2
    Uninstalling future-0.15.2:
      Successfully uninstalled future-0.15.2
  Found existing installation: retriever 2.0.de
    Uninstalling retriever-2.0.de:
      Successfully uninstalled retriever-2.0.de
Successfully installed future-0.16.0 retriever-2.0.0

Now in R with a freshly installed rdataretriever package, it can't seem to find the dataset scripts.

[1] "Failed to load script: abalone_age (C:/Users/hurlbert/.retriever/scripts/)"                               
  [2] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/abalone_age.py, line 7) "                 
  [3] "Failed to load script: antarctic_breed_bird (C:/Users/hurlbert/.retriever/scripts/)"                      
  [4] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/antarctic_breed_bird.py, line 7) "        
  [5] "Failed to load script: biodiversity_response (C:/Users/hurlbert/.retriever/scripts/)"                     
  [6] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/biodiversity_response.py, line 7) "       
  [7] "Failed to load script: bird_migration_data (C:/Users/hurlbert/.retriever/scripts/)"                       
  [8] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/bird_migration_data.py, line 7) "         
  [9] "Failed to load script: bird_size (C:/Users/hurlbert/.retriever/scripts/)"                                 
 [10] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/bird_size.py, line 7) "                   
 [11] "Failed to load script: breast_cancer_wi (C:/Users/hurlbert/.retriever/scripts/)"                          
 [12] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/breast_cancer_wi.py, line 7) "            
 [13] "Failed to load script: butterfly_population_network (C:/Users/hurlbert/.retriever/scripts/)"              
 [14] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/butterfly_population_network.py, line 7) "
 [15] "Failed to load script: car_eval (C:/Users/hurlbert/.retriever/scripts/)"                                  
 [16] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/car_eval.py, line 7) "                    
 [17] "Failed to load script: chytr_disease_distr (C:/Users/hurlbert/.retriever/scripts/)"                       
 [18] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/chytr_disease_distr.py, line 6) "         
 [19] "Failed to load script: community_abundance_misc (C:/Users/hurlbert/.retriever/scripts/)"                  
 [20] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/community_abundance_misc.py, line 9) "    
 [21] "Failed to load script: dicerandra_frutescens (C:/Users/hurlbert/.retriever/scripts/)"                     
 [22] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/dicerandra_frutescens.py, line 7) "       
 [23] "Failed to load script: elton_traits (C:/Users/hurlbert/.retriever/scripts/)"                              
 [24] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/elton_traits.py, line 7) "                
 [25] "Failed to load script: fish_parasite_hosts (C:/Users/hurlbert/.retriever/scripts/)"                       
 [26] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/fish_parasite_hosts.py, line 9) "         
 [27] "Failed to load script: forest_biomass_china (C:/Users/hurlbert/.retriever/scripts/)"                      
 [28] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_biomass_china.py, line 7) "        
 [29] "Failed to load script: forest_fires_portugal (C:/Users/hurlbert/.retriever/scripts/)"                     
 [30] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_fires_portugal.py, line 7) "       
 [31] "Failed to load script: forest_plots_michigan (C:/Users/hurlbert/.retriever/scripts/)"                     
 [32] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_plots_michigan.py, line 7) "       
 [33] "Failed to load script: fray_jorge_ecology (C:/Users/hurlbert/.retriever/scripts/)"                        
 [34] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/fray_jorge_ecology.py, line 7) "          
 [35] "Failed to load script: great_basin_mammal_abundance (C:/Users/hurlbert/.retriever/scripts/)"              
 [36] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/great_basin_mammal_abundance.py, line 6) "
 [37] "Failed to load script: home_ranges (C:/Users/hurlbert/.retriever/scripts/)"                               
 [38] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/home_ranges.py, line 7) "                 
 [39] "Failed to load script: iris (C:/Users/hurlbert/.retriever/scripts/)"                                      
 [40] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/iris.py, line 7) "                        
 [41] "Failed to load script: leaf_herbivory (C:/Users/hurlbert/.retriever/scripts/)"                            
 [42] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/leaf_herbivory.py, line 7) "              
 [43] "Failed to load script: macroalgal_communities (C:/Users/hurlbert/.retriever/scripts/)"                    
 [44] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/macroalgal_communities.py, line 6) "      
 [45] "Failed to load script: macrocystis_variation (C:/Users/hurlbert/.retriever/scripts/)"                     
 [46] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/macrocystis_variation.py, line 7) "       
 [47] "Failed to load script: mammal_community_db (C:/Users/hurlbert/.retriever/scripts/)"                       
 [48] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_community_db.py, line 7) "         
 [49] "Failed to load script: mammal_diet (C:/Users/hurlbert/.retriever/scripts/)"                               
 [50] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_diet.py, line 10) "                
 [51] "Failed to load script: mammal_life_hist (C:/Users/hurlbert/.retriever/scripts/)"                          
 [52] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_life_hist.py, line 7) "            
 [53] "Failed to load script: mammal_masses (C:/Users/hurlbert/.retriever/scripts/)"                             
 [54] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_masses.py, line 7) "               
 [55] "Failed to load script: mammal_metabolic_rate (C:/Users/hurlbert/.retriever/scripts/)"                     
 [56] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_metabolic_rate.py, line 7) "       
 [57] "Failed to load script: mapped_plant_quads_co (C:/Users/hurlbert/.retriever/scripts/)"                     
 [58] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_co.py, line 7) "       
 [59] "Failed to load script: mapped_plant_quads_id (C:/Users/hurlbert/.retriever/scripts/)"                     
 [60] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_id.py, line 7) "       
 [61] "Failed to load script: mapped_plant_quads_ks (C:/Users/hurlbert/.retriever/scripts/)"                     
 [62] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_ks.py, line 7) "       
 [63] "Failed to load script: mapped_plant_quads_mt (C:/Users/hurlbert/.retriever/scripts/)"                     
 [64] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_mt.py, line 9) "       
 [65] "Failed to load script: marine_recruitment_data (C:/Users/hurlbert/.retriever/scripts/)"                   
 [66] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/marine_recruitment_data.py, line 7) "     
 [67] "Failed to load script: mediter_basin_plant_traits (C:/Users/hurlbert/.retriever/scripts/)"                
 [68] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mediter_basin_plant_traits.py, line 7) "  
 [69] "Failed to load script: mt_st_helens_veg (C:/Users/hurlbert/.retriever/scripts/)"                          
 [70] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mt_st_helens_veg.py, line 7) "            
 [71] "Failed to load script: nematode_traits (C:/Users/hurlbert/.retriever/scripts/)"                           
 [72] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/nematode_traits.py, line 7) "             
 [73] "Failed to load script: ngreatplains-flowering-dates (C:/Users/hurlbert/.retriever/scripts/)"              
 [74] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/ngreatplains-flowering-dates.py, line 7) "
 [75] "Failed to load script: nyc_tree_count (C:/Users/hurlbert/.retriever/scripts/)"                            
 [76] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/nyc_tree_count.py, line 7) "              
 [77] "Failed to load script: phytoplankton_size (C:/Users/hurlbert/.retriever/scripts/)"                        
 [78] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/phytoplankton_size.py, line 7) "          
 [79] "Failed to load script: plant_comp_ok (C:/Users/hurlbert/.retriever/scripts/)"                             
 [80] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_comp_ok.py, line 7) "               
 [81] "Failed to load script: plant_occur_oosting (C:/Users/hurlbert/.retriever/scripts/)"                       
 [82] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_occur_oosting.py, line 7) "         
 [83] "Failed to load script: plant_taxonomy_us (C:/Users/hurlbert/.retriever/scripts/)"                         
 [84] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_taxonomy_us.py, line 7) "           
 [85] "Failed to load script: poker_hands (C:/Users/hurlbert/.retriever/scripts/)"                               
 [86] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/poker_hands.py, line 7) "                 
 [87] "Failed to load script: portal-dev (C:/Users/hurlbert/.retriever/scripts/)"                                
 [88] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/portal-dev.py, line 7) "                  
 [89] "Failed to load script: portal (C:/Users/hurlbert/.retriever/scripts/)"                                    
 [90] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/portal.py, line 11) "                     
 [91] "Failed to load script: predator_prey_body_ratio (C:/Users/hurlbert/.retriever/scripts/)"                  
 [92] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/predator_prey_body_ratio.py, line 6) "    
 [93] "Failed to load script: species_exctinction_rates (C:/Users/hurlbert/.retriever/scripts/)"                 
 [94] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/species_exctinction_rates.py, line 7) "   
 [95] "Failed to load script: streamflow_conditions (C:/Users/hurlbert/.retriever/scripts/)"                     
 [96] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/streamflow_conditions.py, line 6) "       
 [97] "Failed to load script: tree_canopy_geometries (C:/Users/hurlbert/.retriever/scripts/)"                    
 [98] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/tree_canopy_geometries.py, line 7) "      
 [99] "Failed to load script: turtle_offspring_nesting (C:/Users/hurlbert/.retriever/scripts/)"                  
[100] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/turtle_offspring_nesting.py, line 7) "    
[101] "Failed to load script: veg_plots_sdl (C:/Users/hurlbert/.retriever/scripts/)"                             
[102] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/veg_plots_sdl.py, line 10) "              
[103] "Failed to load script: wine_composition (C:/Users/hurlbert/.retriever/scripts/)"                          
[104] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/wine_composition.py, line 10) "           
[105] "Failed to load script: wine_quality (C:/Users/hurlbert/.retriever/scripts/)"                              
[106] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/wine_quality.py, line 7) "                
[107] "Failed to load script: abalone_age (C:/Users/hurlbert/.retriever/scripts/)"                               
[108] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/abalone_age.py, line 7) "                 
[109] "Failed to load script: antarctic_breed_bird (C:/Users/hurlbert/.retriever/scripts/)"                      
[110] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/antarctic_breed_bird.py, line 7) "        
[111] "Failed to load script: biodiversity_response (C:/Users/hurlbert/.retriever/scripts/)"                     
[112] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/biodiversity_response.py, line 7) "       
[113] "Failed to load script: bird_migration_data (C:/Users/hurlbert/.retriever/scripts/)"                       
[114] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/bird_migration_data.py, line 7) "         
[115] "Failed to load script: bird_size (C:/Users/hurlbert/.retriever/scripts/)"                                 
[116] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/bird_size.py, line 7) "                   
[117] "Failed to load script: breast_cancer_wi (C:/Users/hurlbert/.retriever/scripts/)"                          
[118] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/breast_cancer_wi.py, line 7) "            
[119] "Failed to load script: butterfly_population_network (C:/Users/hurlbert/.retriever/scripts/)"              
[120] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/butterfly_population_network.py, line 7) "
[121] "Failed to load script: car_eval (C:/Users/hurlbert/.retriever/scripts/)"                                  
[122] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/car_eval.py, line 7) "                    
[123] "Failed to load script: chytr_disease_distr (C:/Users/hurlbert/.retriever/scripts/)"                       
[124] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/chytr_disease_distr.py, line 6) "         
[125] "Failed to load script: community_abundance_misc (C:/Users/hurlbert/.retriever/scripts/)"                  
[126] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/community_abundance_misc.py, line 9) "    
[127] "Failed to load script: dicerandra_frutescens (C:/Users/hurlbert/.retriever/scripts/)"                     
[128] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/dicerandra_frutescens.py, line 7) "       
[129] "Failed to load script: elton_traits (C:/Users/hurlbert/.retriever/scripts/)"                              
[130] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/elton_traits.py, line 7) "                
[131] "Failed to load script: fish_parasite_hosts (C:/Users/hurlbert/.retriever/scripts/)"                       
[132] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/fish_parasite_hosts.py, line 9) "         
[133] "Failed to load script: forest_biomass_china (C:/Users/hurlbert/.retriever/scripts/)"                      
[134] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_biomass_china.py, line 7) "        
[135] "Failed to load script: forest_fires_portugal (C:/Users/hurlbert/.retriever/scripts/)"                     
[136] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_fires_portugal.py, line 7) "       
[137] "Failed to load script: forest_plots_michigan (C:/Users/hurlbert/.retriever/scripts/)"                     
[138] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/forest_plots_michigan.py, line 7) "       
[139] "Failed to load script: fray_jorge_ecology (C:/Users/hurlbert/.retriever/scripts/)"                        
[140] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/fray_jorge_ecology.py, line 7) "          
[141] "Failed to load script: great_basin_mammal_abundance (C:/Users/hurlbert/.retriever/scripts/)"              
[142] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/great_basin_mammal_abundance.py, line 6) "
[143] "Failed to load script: home_ranges (C:/Users/hurlbert/.retriever/scripts/)"                               
[144] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/home_ranges.py, line 7) "                 
[145] "Failed to load script: iris (C:/Users/hurlbert/.retriever/scripts/)"                                      
[146] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/iris.py, line 7) "                        
[147] "Failed to load script: leaf_herbivory (C:/Users/hurlbert/.retriever/scripts/)"                            
[148] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/leaf_herbivory.py, line 7) "              
[149] "Failed to load script: macroalgal_communities (C:/Users/hurlbert/.retriever/scripts/)"                    
[150] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/macroalgal_communities.py, line 6) "      
[151] "Failed to load script: macrocystis_variation (C:/Users/hurlbert/.retriever/scripts/)"                     
[152] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/macrocystis_variation.py, line 7) "       
[153] "Failed to load script: mammal_community_db (C:/Users/hurlbert/.retriever/scripts/)"                       
[154] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_community_db.py, line 7) "         
[155] "Failed to load script: mammal_diet (C:/Users/hurlbert/.retriever/scripts/)"                               
[156] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_diet.py, line 10) "                
[157] "Failed to load script: mammal_life_hist (C:/Users/hurlbert/.retriever/scripts/)"                          
[158] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_life_hist.py, line 7) "            
[159] "Failed to load script: mammal_masses (C:/Users/hurlbert/.retriever/scripts/)"                             
[160] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_masses.py, line 7) "               
[161] "Failed to load script: mammal_metabolic_rate (C:/Users/hurlbert/.retriever/scripts/)"                     
[162] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mammal_metabolic_rate.py, line 7) "       
[163] "Failed to load script: mapped_plant_quads_co (C:/Users/hurlbert/.retriever/scripts/)"                     
[164] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_co.py, line 7) "       
[165] "Failed to load script: mapped_plant_quads_id (C:/Users/hurlbert/.retriever/scripts/)"                     
[166] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_id.py, line 7) "       
[167] "Failed to load script: mapped_plant_quads_ks (C:/Users/hurlbert/.retriever/scripts/)"                     
[168] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_ks.py, line 7) "       
[169] "Failed to load script: mapped_plant_quads_mt (C:/Users/hurlbert/.retriever/scripts/)"                     
[170] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mapped_plant_quads_mt.py, line 9) "       
[171] "Failed to load script: marine_recruitment_data (C:/Users/hurlbert/.retriever/scripts/)"                   
[172] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/marine_recruitment_data.py, line 7) "     
[173] "Failed to load script: mediter_basin_plant_traits (C:/Users/hurlbert/.retriever/scripts/)"                
[174] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mediter_basin_plant_traits.py, line 7) "  
[175] "Failed to load script: mt_st_helens_veg (C:/Users/hurlbert/.retriever/scripts/)"                          
[176] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/mt_st_helens_veg.py, line 7) "            
[177] "Failed to load script: nematode_traits (C:/Users/hurlbert/.retriever/scripts/)"                           
[178] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/nematode_traits.py, line 7) "             
[179] "Failed to load script: ngreatplains-flowering-dates (C:/Users/hurlbert/.retriever/scripts/)"              
[180] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/ngreatplains-flowering-dates.py, line 7) "
[181] "Failed to load script: nyc_tree_count (C:/Users/hurlbert/.retriever/scripts/)"                            
[182] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/nyc_tree_count.py, line 7) "              
[183] "Failed to load script: phytoplankton_size (C:/Users/hurlbert/.retriever/scripts/)"                        
[184] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/phytoplankton_size.py, line 7) "          
[185] "FaileAvailable datasets : 28"                                                                             
[186] ""                                                                                                         
[187] "amniote-life-hist"                                                                                        
[188] "aquatic-animal-excretion"                                                                                 
[189] "bioclim"                                                                                                  
[190] "biomass-allometry-db"                                                                                     
[191] "breed-bird-survey"                                                                                        
[192] "breed-bird-survey-50stop"                                                                                 
[193] "flensburg-food-web"                                                                                       
[194] "forest-inventory-analysis"                                                                                
[195] "forest-plots-wghats"                                                                                      
[196] "gentry-forest-transects"                                                                                  
[197] "intertidal-abund-me"                                                                                      
[198] "la-selva-trees"                                                                                           
[199] "mammal-super-tree"                                                                                        
[200] "NPN"                                                                                                      
[201] "pantheria"                                                                                                
[202] "plant-life-hist-eu"                                                                                       
[203] "predator-prey-size-marine"                                                                                
[204] "predicts"                                                                                                 
[205] "prism-climate"                                                                                            
[206] "socean-diet-data"                                                                                         
[207] "tree-demog-wghats"                                                                                        
[208] "vertnet"                                                                                                  
[209] "vertnet-amphibians"                                                                                       
[210] "vertnet-birds"                                                                                            
[211] "vertnet-fishes"                                                                                           
[212] "vertnet-mammals"                                                                                          
[213] "vertnet-reptiles"                                                                                         
[214] "wood-density"                                                                                             
[215] "d to load script: plant_comp_ok (C:/Users/hurlbert/.retriever/scripts/)"                                  
[216] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_comp_ok.py, line 7) "               
[217] "Failed to load script: plant_occur_oosting (C:/Users/hurlbert/.retriever/scripts/)"                       
[218] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_occur_oosting.py, line 7) "         
[219] "Failed to load script: plant_taxonomy_us (C:/Users/hurlbert/.retriever/scripts/)"                         
[220] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/plant_taxonomy_us.py, line 7) "           
[221] "Failed to load script: poker_hands (C:/Users/hurlbert/.retriever/scripts/)"                               
[222] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/poker_hands.py, line 7) "                 
[223] "Failed to load script: portal-dev (C:/Users/hurlbert/.retriever/scripts/)"                                
[224] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/portal-dev.py, line 7) "                  
[225] "Failed to load script: portal (C:/Users/hurlbert/.retriever/scripts/)"                                    
[226] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/portal.py, line 11) "                     
[227] "Failed to load script: predator_prey_body_ratio (C:/Users/hurlbert/.retriever/scripts/)"                  
[228] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/predator_prey_body_ratio.py, line 6) "    
[229] "Failed to load script: species_exctinction_rates (C:/Users/hurlbert/.retriever/scripts/)"                 
[230] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/species_exctinction_rates.py, line 7) "   
[231] "Failed to load script: streamflow_conditions (C:/Users/hurlbert/.retriever/scripts/)"                     
[232] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/streamflow_conditions.py, line 6) "       
[233] "Failed to load script: tree_canopy_geometries (C:/Users/hurlbert/.retriever/scripts/)"                    
[234] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/tree_canopy_geometries.py, line 7) "      
[235] "Failed to load script: turtle_offspring_nesting (C:/Users/hurlbert/.retriever/scripts/)"                  
[236] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/turtle_offspring_nesting.py, line 7) "    
[237] "Failed to load script: veg_plots_sdl (C:/Users/hurlbert/.retriever/scripts/)"                             
[238] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/veg_plots_sdl.py, line 10) "              
[239] "Failed to load script: wine_composition (C:/Users/hurlbert/.retriever/scripts/)"                          
[240] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/wine_composition.py, line 10) "           
[241] "Failed to load script: wine_quality (C:/Users/hurlbert/.retriever/scripts/)"                              
[242] "Exception: invalid syntax (C:/Users/hurlbert/.retriever/scripts/wine_quality.py, line 7) "

I get the same output (without line numbers) just typing retriever ls in the command line.

I feel like I've been here before...

Am on Windows 7 32-bit OS using retriever 2.0.0 and Anaconda Python 2.7

UPDATE: As far as I can tell, the scripts all seem to be in the folder where it's looking...

henrykironde commented 7 years ago

Thanks @ahhurlbert, Could you delete the retriever C:/Users/hurlbert/.retriever/ folder and try again. Let me know what you get after deleting and running retriever ls

ahhurlbert commented 7 years ago

Thanks! Ok, the list looks good now.

$ retriever ls
No scripts are currently available. Updating scripts now...
Downloading scripts...
Download Progress: [####################] 100.00%
The retriever is up-to-date

Scripts downloaded.

Available datasets : 81

abalone-age
amniote-life-hist
antarctic-breed-bird
aquatic-animal-excretion
bioclim
biodiversity-response
biomass-allometry-db
bird-migration-data
bird-size
breast-cancer-wi
breed-bird-survey
breed-bird-survey-50stop
butterfly-population-network
car-eval
chytr-disease-distr
community-abundance-misc
dicerandra-frutescens
elton-traits
fish-parasite-hosts
flensburg-food-web
forest-biomass-china
forest-fires-portugal
forest-inventory-analysis
forest-plots-michigan
forest-plots-wghats
fray-jorge-ecology
gentry-forest-transects
great-basin-mammal-abundance
home-ranges
intertidal-abund-me
iris
la-selva-trees
leaf-herbivory
macroalgal_communities
macrocystis-variation
mammal-community-db
mammal-diet
mammal-life-hist
mammal-masses
mammal-metabolic-rate
mammal-super-tree
mapped-plant-quads-co
mapped-plant-quads-id
mapped-plant-quads-ks
mapped-plant-quads-mt
marine-recruitment-data
mediter-basin-plant-traits
mt-st-helens-veg
nematode-traits
ngreatplains-flowering-dates
NPN
nyc-tree-count
pantheria
phytoplankton-size
plant-comp-ok
plant-life-hist-eu
plant-occur-oosting
plant-taxonomy-us
poker-hands
portal
portal-dev
predator-prey-body-ratio
predator-prey-size-marine
predicts
prism-climate
socean-diet-data
species-exctinction-rates
streamflow-conditions
tree-canopy-geometries
tree-demog-wghats
turtle-offspring-nesting
veg-plots-sdl
vertnet
vertnet-amphibians
vertnet-birds
vertnet-fishes
vertnet-mammals
vertnet-reptiles
wine-composition
wine-quality
wood-density

Similarly, in R, I now get a reasonable looking list (although "Available datasets : 81" and "" are the first two items in the list and probably shouldn't be.

Now, a new problem , I'll open a new issue.

ethanwhite commented 7 years ago

Thanks @ahhurlbert.

Can you open an issue in the rdataretriever issue about the first two items in the list?

For the original problem one good general debugging trick is the run retriever reset all (which just deletes the .retriever folder) followed by retriever update from the command line. If things have gotten out of whack with data or scripts, like in this case, it will fix things.