R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> setwd("/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project")
> gcube_token<<-"0b999a4f-f160-4697-9166-b68e0071f128-843339462"
> gcube_username<<-"paultaconet"
> gcube_context<<-"/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab"
> source('/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project/96febf27-7f5f-418b-a41c-175871d821b9main')
setting working directory
setting working directory /home/gcube/tomcat/webapps/wps/ecocfg/rscr_88ca8e87-5f0c-4ae4-abe4-03b2a1fa6b4d/sai_project 
setting working directory OK
setting values to parameters
setting values to parameters OK
create metadata_and_parameterization object
create metadata_and_parameterization object OK
source R scripts to use in the algo
source R scripts to use in the algo OK
Start generating dataset
Starting generation of the dataset...
Begin: Retrieving primary datasets from Tuna atlas DB... 
Retrieving IOTC georeferenced dataset from the Tuna atlas database...

retrieving dataset 
dimension schooltype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
dimension catchtype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
retrieving dataset 
dimension schooltype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
dimension catchtype is missing in the dataset. Adding this dimension to the dataset and filling it with values UNK (unknown)
retrieving dataset 
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
Retrieving RFMOs nominal catch...

retrieving dataset Retrieving RFMOs nominal catch OK
Retrieving primary datasets from the Tuna atlas DB OK
Mapping code lists...
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. 
Mapping code lists OK
Mapping code lists of georeferenced georef_dataset datasets...

 mapping dimension gear with code list mapping
 mapping dimension species with code list mapping
 mapping dimension flag with code list mapping
 mapping dimension schooltype with code list mapping
 mapping dimension catchtype with code list mappingMapping code lists of georeferenced georef_dataset datasets OK
Mapping code lists of nominal georef_dataset datasets...

 mapping dimension gear with code list mapping
 mapping dimension species with code list mapping
 mapping dimension flag with code list mappingMapping code lists of nominal georef_dataset datasets OK
Raising georeferenced dataset to nominal dataset
Raising georeferenced dataset of IOTC, ICCAT and IATTC - if included in the Tuna Atlas - by gear,flag,species,year,source_authority,unit
Raising georeferenced dataset to nominal dataset OK
Aggregating data that are defined on quadrants or areas inferior to 5° quadrant resolution to corresponding 5° quadrant...
Aggregating data that are defined on quadrants or areas inferior to 5° quadrant resolution to corresponding 5° quadrant OK
Reallocating data that are in land areas...
Please ignore here-under warning messages 'unrecognized PostgreSQL field type unknown'Removing data that are in land areas...
Removing data that are in land areas OK
End: Your tuna atlas dataset has been created! Your output data.frame is called 'dataset' 
End generation of the dataset
Uploading indian_ocean_catch_1m_1952_11_01_2016_01_01_tunaatlasird.R to /Workspace/MySpecialFolders/FAO_TunaAtlas/R_scripts/datasets_creation 
null
Loading required package: dplyr

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

Loading required package: data.table

Attaching package: ‘data.table’

The following objects are masked from ‘package:dplyr’:

    between, first, last

Loading required package: DBI
Joining, by = c("source_authority", "gear")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "species")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "flag")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "schooltype")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "catchtype")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "gear")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "species")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "flag")
Using 'sum_value_by_dimension' as value column. Use 'value.var' to override
Joining, by = c("source_authority", "flag", "gear", "species", "unit", "year")
Joining, by = "unit"
Joining, by = "unit"
Joining, by = "unit"
Joining, by = "unit"
Joining, by = "unit"
trying URL 'https://raw.githubusercontent.com/ptaconet/rtunaatlas_scripts/master/tunaatlas_world/create_own_tuna_atlas/create_own_tuna_atlas_catch_effort.R'
Content type 'text/plain; charset=utf-8' length 27047 bytes (26 KB)
==================================================
downloaded 26 KB

Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
Error in authenticate(username, token, type = "basic") : 
  object 'username' not found
Calls: source ... request_build -> as.request -> authenticate -> stopifnot
In addition: Warning messages:
1: In postgresqlExecStatement(conn, statement, ...) :
  RS-DBI driver warning: (unrecognized PostgreSQL field type unknown (id:705) in column 2)
2: In postgresqlExecStatement(conn, statement, ...) :
  RS-DBI driver warning: (unrecognized PostgreSQL field type unknown (id:705) in column 3)
Execution halted
null
