Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(eva3dm)
  > 
  > test_check("eva3dm")
  calculating wind speed ...
  calculating wind direction...
  VVIbes has only 0 valid observations (lesser than 8 obs)
  Ibirapuera not found in observation input
  Americana has 227 valid observations
  using 0 for min cutoff
  227 values left
  using 999 for max cutoff
  227 values left
  using 0 for min NME cutoff
  227 values left
  using 935 for max NME cutoff
  227 values left
  Terradonunca not found in observation input
  Americana not found in model input
  zeros contains only zeros (or constant values) and NA values for model
  zeros contains only zeros (or constant values) and NA values for observations
  zeros contains only zeros (or constant values) and NA values for observations
  combining all sites...
  considering a fair comparison for other domain...
  Americana  SAndre  VVIbes  zero  zeros  ...
  ALL has 914 valid observations
  combining all sites...
  considering a fair comparison for other domain...
  Americana  SAndre  VVIbes  zero  zeros  ...
  ALL has 914 valid observations
  using model in obs 
  combining all sites...
  Americana  SAndre  VVIbes  zero  zeros  ...
  ALL has 914 valid observations
  using model in names(obs) 
  combining all sites...
  Americana  SAndre  VVIbes  zero  zeros  ...
  ALL has 914 valid observations
                           n      Obs       Sim          r       IOA        FA2
  VVIbes                   0       NA        NA         NA        NA         NA
  Ibirapuera               0       NA        NA         NA        NA         NA
  am 2                   227 440.9295 378.18197  0.6492022 0.4366783 1.00000000
  Terradonunca             0       NA        NA         NA        NA         NA
  Americana                0       NA        NA         NA        NA         NA
  model zero               0       NA        NA         NA        NA         NA
  obs zero                 0       NA        NA         NA        NA         NA
  obs cke                  0       NA        NA         NA        NA         NA
  all fair               914 155.6685  39.70511 -0.3543786 0.3421893 0.03829322
  all fair 2             914 155.6685  39.70511 -0.3543786 0.3421893 0.03829322
  all model in obs       914 155.6685  39.70511 -0.3543786 0.3421893 0.03829322
  all names model in obs 914 155.6685  39.70511 -0.3543786 0.3421893 0.03829322
                              RMSE         MB        ME   NMB (%)   NME (%)
  VVIbes                        NA         NA        NA        NA        NA
  Ibirapuera                    NA         NA        NA        NA        NA
  am 2                    66.89005  -62.74754  62.74754 -14.23074  14.23074
  Terradonunca                  NA         NA        NA        NA        NA
  Americana                     NA         NA        NA        NA        NA
  model zero                    NA         NA        NA        NA        NA
  obs zero                      NA         NA        NA        NA        NA
  obs cke                       NA         NA        NA        NA        NA
  all fair               235.09955 -115.96338 177.83271 -74.49381 114.23809
  all fair 2             235.09955 -115.96338 177.83271 -74.49381 114.23809
  all model in obs       235.09955 -115.96338 177.83271 -74.49381 114.23809
  all names model in obs 235.09955 -115.96338 177.83271 -74.49381 114.23809
  Americana has 227 valid observations
  SAndre has 207 valid observations
  VVIbes has only 0 valid observations (lesser than 8 obs)
  georeferencing stats at sites 
  extracting series of o3 field 4d for 2 points
  dim of lat/lon: 125 125 
  used dim of lat/lon: 125 125 
  inside lat / lon range: 2 points
  calculating distances...
  extracting series of o3 field 4d for 2 points
  dim of lat/lon: 125 125 
  used dim of lat/lon: 125 125 
  using i & j to extract points:
               lat       lon    name agency            class         city state
  BA0001 -12.68638 -38.33360 Gravatá  INEMA Não classificada     Camaçari    BA
  BA0002 -12.63026 -38.35853   Cobre  INEMA Não classificada Dias D'Ávila    BA
         start   i  j model_lat model_lon
  BA0001  2000 110 67 -12.70324 -38.39191
  BA0002  2000 110 67 -12.70324 -38.39191
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 
  output: /tmp/RtmpLwgjIV/SERIE/serie.o3.Rds 
  extracting series of o3 field 4d for 5 points
  dim of lat/lon: 125 125 
  used dim of lat/lon: 125 125 
  inside lat / lon range: 5 points
  calculating distances...
  * station Gravatá ouside the domain
  * station Cobre ouside the domain
  * station Areias ouside the domain
  * station Lamarão ouside the domain
               lon       lat   i  j model_lat model_lon
  Escola -38.27318 -12.63532 110 67 -12.70324 -38.39191
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 
  output: /tmp/RtmpLwgjIV/SERIE/serie.o3.Rds 
  extracting series of o3 field 4d for 5 points
  dim of lat/lon: 125 125 
  used dim of lat/lon: 125 125 
  inside lat / lon range: 5 points
  calculating distances...
  * station Gravatá ouside the domain
  * station Cobre ouside the domain
  * station Areias ouside the domain
  * station Lamarão ouside the domain
               lon       lat   i  j model_lat model_lon
  Escola -38.27318 -12.63532 110 67 -12.70324 -38.39191
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 
  reading o3 : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 
  output: /tmp/RtmpLwgjIV/SERIE/serie.o3.Rds 
  extracting mean of o3 field 4d 
  reading: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrf.day1.o3.nc file 1 of 1 
  min: 2.123069e-05 mean: 0.007767247 max: 0.03175572 
  total times: 1 
  output: /tmp/RtmpLwgjIV/MEAN/mean.o3.nc 
  extracting 8h max of o3 field 3d units: ug m-3 
  reading: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/test_small_o3.nc file 1 of 1 
  min: 2.010639e-13 mean: 23.42075 max: 99.85495 
  total times: 24 
  output: /tmp/RtmpLwgjIV/MDA8/mean.o3.nc 
  terra 1.7.83
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  writing XLAT in /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrfinput_d01
  Error in R_nc4_open: Read-only file system
  [1] "Error in nc_open trying to open file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrfinput_d01 (setting rv$error TRUE and returning because return_on_error==TRUE)"
  reading /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/sat_cat.csv 
  reading /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/sat_cat.txt 
  writing /tmp/RtmpLwgjIV/s/sat_cat.csv 
  writing /tmp/RtmpLwgjIV/s/sat_cat.txt 
  croping m with o 
  removing 6 points for the model (y) boundaryes ...
  interpolating obs. (x) to model grid (y)...
  removing 6 points for the model (y) boundaryes ...
  interpolating obs. (x) to model grid (y)...
  seting min value to 2 
  seting max value to 110 
  using 0.05 for min cutoff
  97 values left
  using 3 for max cutoff
  97 values left
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : link wrf output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_wrf.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie()
   r-script /tmp/RtmpLwgjIV/POST/extract_inpet.R : source code to extract inmet using eva3dm::extract_serie()
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : link wrf output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_wrf.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie()
   folder  /tmp/RtmpLwgjIV/POST/CAMx/case : link CAMx output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_CAMx.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_camx.R : source code to extract time-series from AERONET site locations using eva3dm::extract_serie()
   folder  /tmp/RtmpLwgjIV/POST/CAMx/case : link CAMx output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_CAMx.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_camx.R : source code to extract time-series from AERONET site locations using eva3dm::extract_serie()
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : link wrf output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_wrfchem.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie()
   r-script /tmp/RtmpLwgjIV/POST/extract_aq.R : source code to extract AQ stations from Brazil using eva3dm::extract_serie()
   r-script /tmp/RtmpLwgjIV/POST/extract_pm.R : source code to extract PM compositon from AERONET sites using eva3dm::extract_serie()
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : link wrf output files here!
   bash  /tmp/RtmpLwgjIV/POST/post-R_exp.sh : post processing job script
   r-script /tmp/RtmpLwgjIV/POST/extract_expr.R : source code to extract metar using eva3dm::extract_serie()
   new locations can be added to the data.frame with the list of sites.
   folder  /tmp/RtmpLwgjIV/POST/ : copy wrfinput_d01 gere!
   folder  /tmp/RtmpLwgjIV/POST/METAR : destination folder
   r-script /tmp/RtmpLwgjIV/POST/download_METAR.R : script that download metar data using riem package and information from eva3dm and wrfinput_d01 file
   r-script /tmp/RtmpLwgjIV/POST/all_tables.R : setup and run script
   r-script /tmp/RtmpLwgjIV/POST/table_metar_T2.R : evaluation of Temperature using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_Q2.R : evaluation of absolute humidity using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_WS.R : evaluation of wind speed using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_WD.R : evaluation of wind direction using METAR
   r-script /tmp/RtmpLwgjIV/POST/all_tables.R : setup and run script
   r-script /tmp/RtmpLwgjIV/POST/table_metar_T2.R : evaluation of Temperature using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_Q2.R : evaluation of absolute humidity using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_WS.R : evaluation of wind speed using METAR
   r-script /tmp/RtmpLwgjIV/POST/table_metar_WD.R : evaluation of wind direction using METAR
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : link WRF or CAMx post-rocessed output here!
   r-script /tmp/RtmpLwgjIV/POST/all_tables.R : setup and run script
   r-script /tmp/RtmpLwgjIV/POST/table_aq_o3.R : evaluation of hourly 8h O3
   r-script /tmp/RtmpLwgjIV/POST/table_aq_max_o3.R : evaluation of daily max 8h O3
   r-script /tmp/RtmpLwgjIV/POST/table_aq_pm2.5.R : evaluation of daily pm2.5
   NOTE 1: Other scripts in all_tables.R not provided, use previous as template
   NOTE 2: other templates provide templates for metar
   folder  /tmp/RtmpLwgjIV/POST/WRF/case : copy wrf post-proced files here!
   folder  /tmp/RtmpLwgjIV/POST/GPCP : folder to copy satellite data here!
   r-script /tmp/RtmpLwgjIV/POST/table_GPCP_rain.R : script for satellite evaluation (CHANGE the file names!!)
   bash  /tmp/RtmpLwgjIV/POST/post-sate.sh : post processing for satellite evaluation using CDO
  processing hourly data ... 
  processing 8-hour moving avarage ... 
  processing daily maximum ... 
  processing hourly data ... 
  processing 8-hour moving avarage ... 
  processing hourly data ... 
  processing daily statistcis ... 
  File /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrfinput_d01 (NC_FORMAT_CLASSIC):
  
       3 variables (excluding dimension variables):
          char Times[DateStrLen,Time]   
          float XLAT[west_east,south_north]   
              MemoryOrder: XY
              description: LATITUDE, SOUTH IS NEGATIVE
              units: degree north
              stagger: 
              FieldType: 104
          float XLONG[west_east,south_north]   
              MemoryOrder: XY
              description: LONGITUDE, WEST IS NEGATIVE
              units: degree east
              stagger: 
              FieldType: 104
  
       4 dimensions:
          DateStrLen  Size:19 
          Time  Size:1   *** is unlimited *** 
          west_east  Size:149 
          south_north  Size:99 
  
      79 global attributes:
          TITLE:  OUTPUT FROM REAL_EM V3.9.1.1 PREPROCESSOR
          START_DATE: 2011-08-01_00:00:00
          SIMULATION_START_DATE: 2011-08-01_00:00:00
          WEST-EAST_GRID_DIMENSION: 150
          SOUTH-NORTH_GRID_DIMENSION: 100
          BOTTOM-TOP_GRID_DIMENSION: 35
          DX: 9000
          DY: 9000
          GRIDTYPE: C
          DIFF_OPT: 1
          KM_OPT: 4
          DAMP_OPT: 3
          DAMPCOEF: 0.200000002980232
          KHDIF: 0
          KVDIF: 0
          MP_PHYSICS: 10
          RA_LW_PHYSICS: 4
          RA_SW_PHYSICS: 4
          SF_SFCLAY_PHYSICS: 1
          SF_SURFACE_PHYSICS: 2
          BL_PBL_PHYSICS: 1
          CU_PHYSICS: 11
          SF_LAKE_PHYSICS: 0
          SURFACE_INPUT_SOURCE: 1
          SST_UPDATE: 0
          GRID_FDDA: 0
          GFDDA_INTERVAL_M: 0
          GFDDA_END_H: 0
          GRID_SFDDA: 0
          SGFDDA_INTERVAL_M: 0
          SGFDDA_END_H: 0
          HYPSOMETRIC_OPT: 2
          USE_THETA_M: 0
          USE_MAXW_LEVEL: 0
          USE_TROP_LEVEL: 0
          GWD_OPT: 0
          SF_URBAN_PHYSICS: 1
          SF_OCEAN_PHYSICS: 0
          SIMULATION_INITIALIZATION_TYPE: REAL-DATA CASE
          WEST-EAST_PATCH_START_UNSTAG: 1
          WEST-EAST_PATCH_END_UNSTAG: 149
          WEST-EAST_PATCH_START_STAG: 1
          WEST-EAST_PATCH_END_STAG: 150
          SOUTH-NORTH_PATCH_START_UNSTAG: 1
          SOUTH-NORTH_PATCH_END_UNSTAG: 99
          SOUTH-NORTH_PATCH_START_STAG: 1
          SOUTH-NORTH_PATCH_END_STAG: 100
          BOTTOM-TOP_PATCH_START_UNSTAG: 1
          BOTTOM-TOP_PATCH_END_UNSTAG: 34
          BOTTOM-TOP_PATCH_START_STAG: 1
          BOTTOM-TOP_PATCH_END_STAG: 35
          GRID_ID: 1
          PARENT_ID: 1
          I_PARENT_START: 1
          J_PARENT_START: 1
          PARENT_GRID_RATIO: 1
          DT: 45
          CEN_LAT: -23.5499954223633
          CEN_LON: -45
          TRUELAT1: -23
          TRUELAT2: -24
          MOAD_CEN_LAT: -23.5499954223633
          STAND_LON: -45
          POLE_LAT: 90
          POLE_LON: 0
          GMT: 0
          JULYR: 2011
          JULDAY: 213
          MAP_PROJ: 1
          MAP_PROJ_CHAR: Lambert Conformal
          MMINLU: MODIFIED_IGBP_MODIS_NOAH
          NUM_LAND_CAT: 21
          ISWATER: 17
          ISLAKE: 21
          ISICE: 15
          ISURBAN: 13
          ISOILWATER: 14
          HYBRID_OPT: -1
          ETAC: 0
  global attributes:
  TITLE START_DATE SIMULATION_START_DATE WEST-EAST_GRID_DIMENSION SOUTH-NORTH_GRID_DIMENSION BOTTOM-TOP_GRID_DIMENSION DX DY GRIDTYPE DIFF_OPT KM_OPT DAMP_OPT DAMPCOEF KHDIF KVDIF MP_PHYSICS RA_LW_PHYSICS RA_SW_PHYSICS SF_SFCLAY_PHYSICS SF_SURFACE_PHYSICS BL_PBL_PHYSICS CU_PHYSICS SF_LAKE_PHYSICS SURFACE_INPUT_SOURCE SST_UPDATE GRID_FDDA GFDDA_INTERVAL_M GFDDA_END_H GRID_SFDDA SGFDDA_INTERVAL_M SGFDDA_END_H HYPSOMETRIC_OPT USE_THETA_M USE_MAXW_LEVEL USE_TROP_LEVEL GWD_OPT SF_URBAN_PHYSICS SF_OCEAN_PHYSICS SIMULATION_INITIALIZATION_TYPE WEST-EAST_PATCH_START_UNSTAG WEST-EAST_PATCH_END_UNSTAG WEST-EAST_PATCH_START_STAG WEST-EAST_PATCH_END_STAG SOUTH-NORTH_PATCH_START_UNSTAG SOUTH-NORTH_PATCH_END_UNSTAG SOUTH-NORTH_PATCH_START_STAG SOUTH-NORTH_PATCH_END_STAG BOTTOM-TOP_PATCH_START_UNSTAG BOTTOM-TOP_PATCH_END_UNSTAG BOTTOM-TOP_PATCH_START_STAG BOTTOM-TOP_PATCH_END_STAG GRID_ID PARENT_ID I_PARENT_START J_PARENT_START PARENT_GRID_RATIO DT CEN_LAT CEN_LON TRUELAT1 TRUELAT2 MOAD_CEN_LAT STAND_LON POLE_LAT POLE_LON GMT JULYR JULDAY MAP_PROJ MAP_PROJ_CHAR MMINLU NUM_LAND_CAT ISWATER ISLAKE ISICE ISURBAN ISOILWATER HYBRID_OPT ETACvariable Times attritutes:
  not found
  XLAT attribute units:
  degree north
  global attribute DT:
  45
  Error in R_nc4_open: Read-only file system
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rast.R:9:3'): rast based functions are ok ──────────────────────
  Error in `ncdf4::ncatt_get(nc = neto, varid = name, attname = "MemoryOrder")`: Error, first passed argument must be an object of class ncdf4
  Backtrace:
      ▆
   1. └─eva3dm::rast_to_netcdf(r = r, file = wrf, name = "XLAT") at test-rast.R:9:3
   2.   └─ncdf4::ncatt_get(nc = neto, varid = name, attname = "MemoryOrder")
  ── Error ('test-utils.R:11:3'): utility functios are functional! ───────────────
  Error in `ncdf4::nc_open(filename = file, write = to_write)`: Error in nc_open trying to open file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eva3dm/extdata/wrfinput_d01 (return_on_error= FALSE )
  Backtrace:
      ▆
   1. └─eva3dm::atr(...) at test-utils.R:11:3
   2.   └─ncdf4::nc_open(filename = file, write = to_write)
  ── Error ('test-utils.R:11:3'): utility functios are functional! ───────────────
  Error in `if (nc$safemode) {
      return()
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─eva3dm::atr(...) at test-utils.R:11:3
   2.   └─ncdf4::nc_close(meta) at test-utils.R:11:3
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted