• using R Under development (unstable) (2024-11-22 r87365)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘eva3dm/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘eva3dm’ version ‘0.99’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘eva3dm’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/6s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/6s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [22s/28s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [8s/18s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/13s] ERROR   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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR