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R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
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Copyright (C) 2017 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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Natural language support but running in an English locale
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> setwd("/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project")
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> gcube_token<<-"0b999a4f-f160-4697-9166-b68e0071f128-843339462"
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> gcube_username<<-"paultaconet"
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> gcube_context<<-"/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab"
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> source('/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project/96febf27-7f5f-418b-a41c-175871d821b9main')
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setting working directory
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setting working directory /home/gcube/tomcat/webapps/wps/ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project
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setting working directory OK
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setting values to parameters
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setting values to parameters OK
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create metadata_and_parameterization object
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create metadata_and_parameterization object OK
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source R scripts to use in the algo
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source R scripts to use in the algo OK
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Start generating dataset
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Starting generation of the dataset...
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Begin: Retrieving primary datasets from Tuna atlas DB...
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Retrieving IOTC georeferenced dataset from the Tuna atlas database...
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retrieving dataset
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dimension schooltype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
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dimension catchtype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
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retrieving dataset
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dimension schooltype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
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dimension catchtype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
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retrieving dataset
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dimension catchtype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)Retrieving IOTC georeferenced dataset from the Tuna atlas database OK
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Retrieving RFMOs nominal catch...
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retrieving dataset Retrieving RFMOs nominal catch OK
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Retrieving primary datasets from the Tuna atlas DB OK
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Mapping code lists...
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Reading the CSV containing the dimensions to map + the names of the code list mapping datasets. Code list mapping datasets must be available in the database.
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Mapping code lists OK
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Mapping code lists of georeferenced georef_dataset datasets...
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mapping dimension gear with code list mapping
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mapping dimension species with code list mapping
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mapping dimension flag with code list mapping
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mapping dimension schooltype with code list mapping
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mapping dimension catchtype with code list mappingMapping code lists of georeferenced georef_dataset datasets OK
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Mapping code lists of nominal georef_dataset datasets...
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mapping dimension gear with code list mapping
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mapping dimension species with code list mapping
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mapping dimension flag with code list mappingMapping code lists of nominal georef_dataset datasets OK
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Raising georeferenced dataset to nominal dataset
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Raising georeferenced dataset of IOTC, ICCAT and IATTC - if included in the Tuna Atlas - by gear,flag,species,year,source_authority,unit
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Raising georeferenced dataset to nominal dataset OK
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Aggregating data that are defined on quadrants or areas inferior to 5° quadrant resolution to corresponding 5° quadrant...
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Aggregating data that are defined on quadrants or areas inferior to 5° quadrant resolution to corresponding 5° quadrant OK
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Reallocating data that are in land areas...
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Please ignore here-under warning messages 'unrecognized PostgreSQL field type unknown'Removing data that are in land areas...
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Removing data that are in land areas OK
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End: Your tuna atlas dataset has been created! Your output data.frame is called 'dataset'
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End generation of the dataset
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Uploading indian_ocean_catch_1m_1952_11_01_2016_01_01_tunaatlasird.R to /Workspace/MySpecialFolders/FAO_TunaAtlas/R_scripts/datasets_creation
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null
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Loading required package: dplyr
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Attaching package: ‘dplyr’
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The following objects are masked from ‘package:stats’:
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filter, lag
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The following objects are masked from ‘package:base’:
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intersect, setdiff, setequal, union
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Loading required package: data.table
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Attaching package: ‘data.table’
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The following objects are masked from ‘package:dplyr’:
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between, first, last
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Loading required package: DBI
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Joining, by = c("source_authority", "gear")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "species")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "flag")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "schooltype")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "catchtype")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "gear")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "species")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "flag")
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Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
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Joining, by = c("source_authority", "flag", "gear", "species", "unit", "year")
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Joining, by = "unit"
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Joining, by = "unit"
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Joining, by = "unit"
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Joining, by = "unit"
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Joining, by = "unit"
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trying URL 'https://raw.githubusercontent.com/ptaconet/rtunaatlas_scripts/master/tunaatlas_world/create_own_tuna_atlas/create_own_tuna_atlas_catch_effort.R'
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Content type 'text/plain; charset=utf-8' length 27047 bytes (26 KB)
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==================================================
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downloaded 26 KB
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Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
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Error in authenticate(username, token, type = "basic") :
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object 'username' not found
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Calls: source ... request_build -> as.request -> authenticate -> stopifnot
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In addition: Warning messages:
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1: In postgresqlExecStatement(conn, statement, ...) :
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RS-DBI driver warning: (unrecognized PostgreSQL field type unknown (id:705) in column 2)
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2: In postgresqlExecStatement(conn, statement, ...) :
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RS-DBI driver warning: (unrecognized PostgreSQL field type unknown (id:705) in column 3)
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Execution halted
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null
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