Method for cloning local NASIS tables into static SQLite file #154

brownag · 2021-01-07T00:59:19Z

Running the NASIS validation on the SQLite backend created by createStaticNASIS not 100% there yet, but this has also identified some methods that do not respect the SS argument.

> test <- lapply(fnames, function(fname) {
+     lapply(fname, function(FUN) {
+       message(sprintf("Testing: %s", FUN))
+       try(get(FUN, envir = as.environment("package:soilDB"))(SS = FALSE, static_path = "testStatic.sqlite"))
+     })
+   })
Testing: fetchNASIS
multiple horizontal datums present, consider using WGS84 coordinates (x_std, y_std)
NOTICE: multiple `labsampnum` values / horizons; see pedon IDs:
S1969NE013001,S1980OK015001
mixing dry colors ... [184 of 8169 horizons]
mixing moist colors ... [284 of 8856 horizons]
-> QC: some fragsize_h values == 76mm, may be mis-classified as cobbles [356 / 11859 records]
replacing missing lower horizon depths with top depth + 1cm ... [140 horizons]
top/bottom depths equal, adding 1cm to bottom depth ... [70 horizons]
-> QC: sites without pedons: use `get('sites.missing.pedons', envir=soilDB.env)` for related usersiteid values
-> QC: duplicate pedons: use `get('dup.pedon.ids', envir=soilDB.env)` for related peiid values
-> QC: horizon errors detected, use `get('bad.pedon.ids', envir=soilDB.env)` for related userpedonid values or `get('bad.horizons', envir=soilDB.env)` for related horizon designations
-> QC: pedons missing bottom hz depths: use `get('missing.bottom.depths', envir=soilDB.env)` for related pedon IDs
-> QC: equal hz top and bottom depths: use `get('top.bottom.equal', envir=soilDB.env)` for related pedon IDs
Testing: getHzErrorsNASIS
Error in get(FUN, envir = as.environment("package:soilDB"))(SS = FALSE,  : 
  unused arguments (SS = FALSE, static_path = "testStatic.sqlite")
In addition: Warning messages:
1: some records are missing rock fragment volume, these have been removed 
2: fragment volume >= 100%
phiid:
4081839
677471
932280
932930 
3: some records are missing artifact volume, these have been removed 
4: all records are missing artifact volume (NULL). buffering result with NA. will be converted to zero if nullFragsAreZero = TRUE. 
Testing: get_RMF_from_NASIS_db
Testing: get_colors_from_NASIS_db
mixing dry colors ... [184 of 8169 horizons]
mixing moist colors ... [284 of 8856 horizons]
Testing: get_component_copm_data_from_NASIS_db
Testing: get_lmuaoverlap_from_NASIS
Testing: get_component_horizon_data_from_NASIS_db
Testing: get_component_data_from_NASIS_db
Testing: get_legend_from_NASIS
Testing: get_mutext_from_NASIS_db
Testing: get_comonth_from_NASIS_db
Testing: get_mapunit_from_NASIS
Testing: get_component_diaghz_from_NASIS_db
Testing: get_component_correlation_data_from_NASIS_db
Testing: get_copedon_from_NASIS_db
some linked pedons not in selected set or local database
Testing: get_component_otherveg_data_from_NASIS_db
Testing: get_component_restrictions_from_NASIS_db
Testing: get_component_cogeomorph_data_from_NASIS_db
Testing: get_component_esd_data_from_NASIS_db
Testing: get_concentrations_from_NASIS_db
Testing: get_cosoilmoist_from_NASIS
Error in get(FUN, envir = as.environment("package:soilDB"))(SS = FALSE,  : 
  unused argument (SS = FALSE)
Testing: get_extended_data_from_NASIS_db
-> QC: some fragsize_h values == 76mm, may be mis-classified as cobbles [356 / 11859 records]
Testing: get_hz_data_from_NASIS_db
NOTICE: multiple `labsampnum` values / horizons; see pedon IDs:
S1969NE013001,S1980OK015001
Testing: get_lablayer_data_from_NASIS_db
Testing: get_labpedon_data_from_NASIS_db
Testing: get_phfmp_from_NASIS_db
Testing: get_projectmapunit_from_NASIS
Testing: get_site_data_from_NASIS_db
multiple horizontal datums present, consider using WGS84 coordinates (x_std, y_std)
Testing: get_text_notes_from_NASIS_db
Testing: get_veg_data_from_NASIS_db
Testing: get_vegplot_location_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
In addition: Warning messages:
1: some records are missing rock fragment volume, these have been removed 
2: fragment volume >= 100%
phiid:
4081839
677471
932280
932930 
3: some records are missing artifact volume, these have been removed 
4: all records are missing artifact volume (NULL). buffering result with NA. will be converted to zero if nullFragsAreZero = TRUE. 
5: In order to query this data you'll need to load all related vegplots to your sites and pedons in NASIS. 
Testing: get_vegplot_tree_si_details_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_species_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_transpecies_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_tree_si_summary_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_textnote_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_trhi_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: get_vegplot_transect_from_NASIS_db
Error in as.character(x) : 
  cannot coerce type 'closure' to vector of type 'character'
Testing: local_NASIS_defined
Error in get(FUN, envir = as.environment("package:soilDB"))(SS = FALSE,  : 
  unused arguments (SS = FALSE, static_path = "testStatic.sqlite")

brownag · 2021-01-07T18:28:31Z

OK, clean bill of health (at least everything runs now with SS = FALSE and static_path = "testStatic.sqlite")

> test <- lapply(fnames, function(fname) {
+     lapply(fname, function(FUN) {
+       message(sprintf("Testing: %s", FUN))
+       if (FUN == "local_NASIS_defined") try(get(FUN, envir = as.environment("package:soilDB"))(static_path = "testStatic.sqlite"))
+       else try(get(FUN, envir = as.environment("package:soilDB"))(SS = selected_set, static_path = "testStatic.sqlite"))
+       # try(get(FUN, envir = as.environment("package:soilDB"))())
+     })
+   })
Testing: fetchNASIS
multiple horizontal datums present, consider using WGS84 coordinates (x_std, y_std)
NOTICE: multiple `labsampnum` values / horizons; see pedon IDs:
S1969NE013001,S1980OK015001
mixing dry colors ... [184 of 8169 horizons]
mixing moist colors ... [284 of 8856 horizons]
-> QC: some fragsize_h values == 76mm, may be mis-classified as cobbles [356 / 11859 records]
replacing missing lower horizon depths with top depth + 1cm ... [140 horizons]
top/bottom depths equal, adding 1cm to bottom depth ... [70 horizons]
-> QC: sites without pedons: use `get('sites.missing.pedons', envir=soilDB.env)` for related usersiteid values
-> QC: duplicate pedons: use `get('dup.pedon.ids', envir=soilDB.env)` for related peiid values
-> QC: horizon errors detected, use `get('bad.pedon.ids', envir=soilDB.env)` for related userpedonid values or `get('bad.horizons', envir=soilDB.env)` for related horizon designations
-> QC: pedons missing bottom hz depths: use `get('missing.bottom.depths', envir=soilDB.env)` for related pedon IDs
-> QC: equal hz top and bottom depths: use `get('top.bottom.equal', envir=soilDB.env)` for related pedon IDs
Testing: getHzErrorsNASIS
multiple horizontal datums present, consider using WGS84 coordinates (x_std, y_std)
NOTICE: multiple `labsampnum` values / horizons; see pedon IDs:
S1969NE013001,S1980OK015001
Testing: get_RMF_from_NASIS_db
Testing: get_colors_from_NASIS_db
mixing dry colors ... [184 of 8169 horizons]
mixing moist colors ... [284 of 8856 horizons]
Testing: get_component_copm_data_from_NASIS_db
Loading required namespace: RODBC
Testing: get_lmuaoverlap_from_NASIS
Testing: get_component_horizon_data_from_NASIS_db
Testing: get_component_data_from_NASIS_db
Testing: get_legend_from_NASIS
Testing: get_mutext_from_NASIS_db
Testing: get_comonth_from_NASIS_db
Testing: get_mapunit_from_NASIS
Testing: get_component_diaghz_from_NASIS_db
Testing: get_component_correlation_data_from_NASIS_db
Testing: get_copedon_from_NASIS_db
some linked pedons not in selected set or local database
Testing: get_component_otherveg_data_from_NASIS_db
Testing: get_component_restrictions_from_NASIS_db
Testing: get_component_cogeomorph_data_from_NASIS_db
Testing: get_component_esd_data_from_NASIS_db
Testing: get_concentrations_from_NASIS_db
Testing: get_cosoilmoist_from_NASIS
Testing: get_extended_data_from_NASIS_db
-> QC: some fragsize_h values == 76mm, may be mis-classified as cobbles [356 / 11859 records]
Testing: get_hz_data_from_NASIS_db
NOTICE: multiple `labsampnum` values / horizons; see pedon IDs:
S1969NE013001,S1980OK015001
Testing: get_lablayer_data_from_NASIS_db
Testing: get_labpedon_data_from_NASIS_db
Testing: get_phfmp_from_NASIS_db
Testing: get_projectmapunit_from_NASIS
Testing: get_site_data_from_NASIS_db
multiple horizontal datums present, consider using WGS84 coordinates (x_std, y_std)
Testing: get_text_notes_from_NASIS_db
Testing: get_veg_data_from_NASIS_db
Testing: get_vegplot_location_from_NASIS_db
Testing: get_vegplot_tree_si_details_from_NASIS_db
Testing: get_vegplot_species_from_NASIS_db
Testing: get_vegplot_transpecies_from_NASIS_db
Testing: get_vegplot_tree_si_summary_from_NASIS_db
Testing: get_vegplot_textnote_from_NASIS_db
Testing: get_vegplot_trhi_from_NASIS_db
Testing: get_vegplot_from_NASIS_db
Testing: get_vegplot_transect_from_NASIS_db
Testing: local_NASIS_defined
There were 11 warnings (use warnings() to see them)

> warnings()
Warning messages:
1: some records are missing rock fragment volume, these have been removed
2: fragment volume >= 100%
phiid:
4081839
677471
932280
932930
3: some records are missing artifact volume, these have been removed
4: all records are missing artifact volume (NULL). buffering result with NA. will be converted to zero if nullFragsAreZero = TRUE.
5: In eval(substitute(expr), e) : NAs introduced by coercion
6: In eval(substitute(expr), e) : NAs introduced by coercion
7: some records are missing rock fragment volume, these have been removed
8: fragment volume >= 100%
phiid:
4081839
677471
932280
932930
9: some records are missing artifact volume, these have been removed
10: all records are missing artifact volume (NULL). buffering result with NA. will be converted to zero if nullFragsAreZero = TRUE.
11: In order to query this data you'll need to load all related vegplots to your sites and pedons in NASIS.

Now, for updating all impacted non-Roxygen documentation to Roxygen.

==> devtools::check(document = FALSE, args = c('--run-donttest'))

-- Building ------------------------- soilDB --
Setting env vars:
* CFLAGS    : -Wall -pedantic
* CXXFLAGS  : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
-----------------------------------------------
WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools 4.0 from https://cran.r-project.org/bin/windows/Rtools/.
v  checking for file 'E:\workspace\soilDB/DESCRIPTION' (442ms)
-  preparing 'soilDB': (28.9s)
v  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts (2.2s)
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'soilDB_2.6.1.tar.gz'
   
-- Checking ------------------------- soilDB --
Setting env vars:
* _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
* _R_CHECK_CRAN_INCOMING_       : FALSE
* _R_CHECK_FORCE_SUGGESTS_      : FALSE
* NOT_CRAN                      : true
-- R CMD check -----------------------------------------------------------------
   R library paths: 
    C:/Users/Andrew.G.Brown/Documents/R/win-library/4.0
    C:/Program Files/R/R-4.0.2/library
-  using log directory 'E:/workspace/soilDB.Rcheck'
-  using R version 4.0.2 (2020-06-22)
-  using platform: x86_64-w64-mingw32 (64-bit)
-  using session charset: ISO8859-1
-  using options '--run-donttest --no-manual --as-cran' (1m 15s)
v  checking for file 'soilDB/DESCRIPTION'
-  checking extension type ... Package
-  this is package 'soilDB' version '2.6.1'
v  checking package namespace information ...
v  checking package dependencies (13.2s)
v  checking if this is a source package ... 
v  checking if there is a namespace
v  checking for .dll and .exe files
v  checking for hidden files and directories ... 
v  checking for portable file names ... 
v  checking whether package 'soilDB' can be installed (36.1s)
v  checking package directory (755ms)
v  checking for future file timestamps (5.9s)
v  checking DESCRIPTION meta-information (565ms)
N  checking top-level files
   Non-standard files/directories found at top level:
     'nasis-targets-master.rda' 'testStatic.sqlite'
v  checking for left-over files ... 
v  checking index information
v  checking package subdirectories ... 
v  checking R files for non-ASCII characters ... 
v  checking R files for syntax errors ... 
v  checking whether the package can be loaded (2.3s)
v  checking whether the package can be loaded with stated dependencies (2.3s)
v  checking whether the package can be unloaded cleanly (2.5s)
v  checking whether the namespace can be loaded with stated dependencies (2.4s)
v  checking whether the namespace can be unloaded cleanly (2.4s)
v  checking loading without being on the library search path (2.6s)
v  checking dependencies in R code (3.4s)
v  checking S3 generic/method consistency (3.9s)
v  checking replacement functions (2.4s)
v  checking foreign function calls (3s)
N  checking R code for possible problems (20.3s)
   fetchNASISLabData: no visible binding for global variable 'static_path'
   fetchVegdata: no visible binding for global variable 'static_path'
   Undefined global functions or variables:
     static_path
v  checking Rd files (1.1s)
v  checking Rd metadata ... 
v  checking Rd line widths ... 
v  checking Rd cross-references (519ms)
v  checking for missing documentation entries (2.5s)
W  checking for code/documentation mismatches (2.9s)
   Codoc mismatches from documentation object 'get_colors_from_NASIS_db':
   get_colors_from_NASIS_db
     Code: function(SS = TRUE, static_path = NULL)
     Docs: function(SS = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_comonth_from_NASIS_db':
   get_comonth_from_NASIS_db
     Code: function(SS = TRUE, fill = FALSE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(SS = TRUE, fill = FALSE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_component_data_from_NASIS_db':
   get_component_data_from_NASIS_db
     Code: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   get_component_restrictions_from_NASIS_db
     Code: function(SS = TRUE, static_path = NULL)
     Docs: function(SS = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_cosoilmoist_from_NASIS':
   get_cosoilmoist_from_NASIS
     Code: function(SS = TRUE, impute = TRUE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(impute = TRUE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       SS static_path
     Mismatches in argument names:
       Position: 1 Code: SS Docs: impute
       Position: 2 Code: impute Docs: stringsAsFactors
   
   Codoc mismatches from documentation object 'get_extended_data_from_NASIS_db':
   get_extended_data_from_NASIS_db
     Code: function(SS = TRUE, nullFragsAreZero = TRUE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(SS = TRUE, nullFragsAreZero = TRUE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_hz_data_from_NASIS_db':
   get_hz_data_from_NASIS_db
     Code: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_lablayer_data_from_NASIS_db':
   get_lablayer_data_from_NASIS_db
     Code: function(SS = TRUE, static_path = NULL)
     Docs: function(SS = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_labpedon_data_from_NASIS_db':
   get_labpedon_data_from_NASIS_db
     Code: function(SS = TRUE, static_path = NULL)
     Docs: function(SS = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_site_data_from_NASIS_db':
   get_site_data_from_NASIS_db
     Code: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors(), static_path = NULL)
     Docs: function(SS = TRUE, stringsAsFactors =
                    default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_soilseries_from_NASIS':
   get_soilseries_from_NASIS
     Code: function(stringsAsFactors = default.stringsAsFactors(),
                    static_path = NULL)
     Docs: function(stringsAsFactors = default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_text_notes_from_NASIS_db':
   get_text_notes_from_NASIS_db
     Code: function(SS = TRUE, fixLineEndings = TRUE, static_path = NULL)
     Docs: function(SS = TRUE, fixLineEndings = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'get_veg_data_from_NASIS_db':
   get_veg_data_from_NASIS_db
     Code: function(SS = TRUE, static_path = NULL)
     Docs: function(SS = TRUE)
     Argument names in code not in docs:
       static_path
   
   Codoc mismatches from documentation object 'uncode':
   uncode
     Code: function(df, invert = FALSE, db = "NASIS", droplevels = FALSE,
                    stringsAsFactors = default.stringsAsFactors(),
                    static_path = NULL)
     Docs: function(df, invert = FALSE, db = "NASIS", droplevels = FALSE,
                    stringsAsFactors = default.stringsAsFactors())
     Argument names in code not in docs:
       static_path
   
W  checking Rd \usage sections (5.6s)
   Undocumented arguments in documentation object 'local_NASIS_defined'
     'static_path'
   
   Functions with \usage entries need to have the appropriate \alias
   entries, and all their arguments documented.
   The \usage entries must correspond to syntactically valid R code.
   See chapter 'Writing R documentation files' in the 'Writing R
   Extensions' manual.
v  checking Rd contents (4.8s)
v  checking for unstated dependencies in examples (921ms)
v  checking contents of 'data' directory (2.9s)
v  checking data for non-ASCII characters (1.2s)
v  checking data for ASCII and uncompressed saves ... 
v  checking examples (4m 8.4s)
   Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
   taxaExtent              18.40   3.70   33.15
   fetchHenry               8.98   0.22   16.98
   fetchNASISWebReport      4.82   0.13   20.57
   fetchSDA_component       2.92   0.02   22.61
   SDA_spatialQuery         2.28   0.51   28.19
   fetchSCAN                1.44   0.02   10.51
   fetchSoilGrids           1.16   0.00    7.68
   OSDquery                 0.93   0.07    6.67
   fetchSDA_spatial         0.82   0.18    7.97
   SDA_query                0.96   0.03    8.53
   fetchKSSL                0.45   0.03   13.86
   fetchOSD                 0.27   0.03    8.68
   uncode                   0.20   0.03   11.94
   fetchRaCA                0.06   0.01   10.04
   mapunit_geom_by_ll_bbox  0.02   0.01    7.28
v  checking for unstated dependencies in 'tests' ... 
-  checking tests ...
E  Running 'testthat.R' [202s] (3m 21.8s)
   Running the tests in 'tests/testthat.R' failed.
   Last 13 lines of output:
       |===================================                                   |  50%
       |                                                                            
       |======================================================================| 100%
     == testthat results  ===========================================================
     [ OK: 289 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 7 ]
     1. Failure: ROSETTA() works (@test-ROSETTA.R#59) 
     2. Failure: ROSETTA() works (@test-ROSETTA.R#62) 
     3. Failure: ROSETTA() works (@test-ROSETTA.R#65) 
     4. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#94) 
     5. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#97) 
     6. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#100) 
     7. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#106) 
     
     Error: testthat unit tests failed
     Execution halted
v  checking for non-standard things in the check directory
v  checking for detritus in the temp directory
   
   See
     'E:/workspace/soilDB.Rcheck/00check.log'
   for details.
   
-- R CMD check results --------------------------------------- soilDB 2.6.1 ----
Duration: 11m 26.7s

> checking tests ...
  See below...

> checking for code/documentation mismatches ... WARNING
  Codoc mismatches from documentation object 'get_colors_from_NASIS_db':
  get_colors_from_NASIS_db
    Code: function(SS = TRUE, static_path = NULL)
    Docs: function(SS = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_comonth_from_NASIS_db':
  get_comonth_from_NASIS_db
    Code: function(SS = TRUE, fill = FALSE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(SS = TRUE, fill = FALSE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_component_data_from_NASIS_db':
  get_component_data_from_NASIS_db
    Code: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  get_component_restrictions_from_NASIS_db
    Code: function(SS = TRUE, static_path = NULL)
    Docs: function(SS = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_cosoilmoist_from_NASIS':
  get_cosoilmoist_from_NASIS
    Code: function(SS = TRUE, impute = TRUE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(impute = TRUE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      SS static_path
    Mismatches in argument names:
      Position: 1 Code: SS Docs: impute
      Position: 2 Code: impute Docs: stringsAsFactors
  
  Codoc mismatches from documentation object 'get_extended_data_from_NASIS_db':
  get_extended_data_from_NASIS_db
    Code: function(SS = TRUE, nullFragsAreZero = TRUE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(SS = TRUE, nullFragsAreZero = TRUE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_hz_data_from_NASIS_db':
  get_hz_data_from_NASIS_db
    Code: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_lablayer_data_from_NASIS_db':
  get_lablayer_data_from_NASIS_db
    Code: function(SS = TRUE, static_path = NULL)
    Docs: function(SS = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_labpedon_data_from_NASIS_db':
  get_labpedon_data_from_NASIS_db
    Code: function(SS = TRUE, static_path = NULL)
    Docs: function(SS = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_site_data_from_NASIS_db':
  get_site_data_from_NASIS_db
    Code: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors(), static_path = NULL)
    Docs: function(SS = TRUE, stringsAsFactors =
                   default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_soilseries_from_NASIS':
  get_soilseries_from_NASIS
    Code: function(stringsAsFactors = default.stringsAsFactors(),
                   static_path = NULL)
    Docs: function(stringsAsFactors = default.stringsAsFactors())
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_text_notes_from_NASIS_db':
  get_text_notes_from_NASIS_db
    Code: function(SS = TRUE, fixLineEndings = TRUE, static_path = NULL)
    Docs: function(SS = TRUE, fixLineEndings = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'get_veg_data_from_NASIS_db':
  get_veg_data_from_NASIS_db
    Code: function(SS = TRUE, static_path = NULL)
    Docs: function(SS = TRUE)
    Argument names in code not in docs:
      static_path
  
  Codoc mismatches from documentation object 'uncode':
  uncode
    Code: function(df, invert = FALSE, db = "NASIS", droplevels = FALSE,
                   stringsAsFactors = default.stringsAsFactors(),
                   static_path = NULL)
    Docs: function(df, invert = FALSE, db = "NASIS", droplevels = FALSE,
                   stringsAsFactors = default.stringsAsFactors())
    Argument names in code not in docs:
      static_path

> checking Rd \usage sections ... WARNING
  Undocumented arguments in documentation object 'local_NASIS_defined'
    'static_path'
  
  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter 'Writing R documentation files' in the 'Writing R
  Extensions' manual.

> checking top-level files ... NOTE
  Non-standard files/directories found at top level:
    'nasis-targets-master.rda' 'testStatic.sqlite'

> checking R code for possible problems ... NOTE
  fetchNASISLabData: no visible binding for global variable 'static_path'
  fetchVegdata: no visible binding for global variable 'static_path'
  Undefined global functions or variables:
    static_path

-- Test failures ------------------------------------------------- testthat ----

> library(testthat)
> library(soilDB)
> 
> test_check("soilDB")
-- 1. Failure: ROSETTA() works (@test-ROSETTA.R#59)  ---------------------------
inherits(r, "data.frame") isn't true.

-- 2. Failure: ROSETTA() works (@test-ROSETTA.R#62)  ---------------------------
nrow(r) == nrow(x) isn't true.

-- 3. Failure: ROSETTA() works (@test-ROSETTA.R#65)  ---------------------------
all(c("theta_r", "theta_s", "alpha", "npar", "ksat") %in% names(r)) isn't true.

-- 4. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#94
r$.rosetta.model[1] == 2 isn't true.

-- 5. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#97
r$.rosetta.model[2] == 3 isn't true.

-- 6. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#10
r$.rosetta.model[3] == 4 isn't true.

-- 7. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#10
is.na(r$theta_r[9]) & (r$.rosetta.model[9] == -1) isn't true.

  |======================================================================| 100%
== testthat results  ===========================================================
[ OK: 289 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 7 ]
1. Failure: ROSETTA() works (@test-ROSETTA.R#59) 
2. Failure: ROSETTA() works (@test-ROSETTA.R#62) 
3. Failure: ROSETTA() works (@test-ROSETTA.R#65) 
4. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#94) 
5. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#97) 
6. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#100) 
7. Failure: correct model selection in the presence of NA (@test-ROSETTA.R#106) 

Error: testthat unit tests failed
Execution halted

1 error x | 2 warnings x | 2 notes x
Error: R CMD check found ERRORs
Execution halted

Exited with status 1.

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/

* Method for cloning local NASIS tables into static SQLite file #149 * local_NASIS_defined: add static_path arg and use RSQLite::dbCanConnect * Add selected set and static path to getHzErrorsNASIS * get_cosoilmoist / get_vegplot should use selected set argument * Special handling for local_NASIS_defined (does not take SS arg) * Add static_path to local_NASIS_defined

@jskovlin

* Convert NASIS-related queries from RODBC->DBI #146 * remove require RODBC * roxygen for fetchNASIS * Color data NA moist state handling * use_sqlite = FALSE is the default for .openNASISchannel * Move VARCHAR(MAX) fields to end of query, per MSSQL specs * fix getHzErrorsNASIS * Validations and tests RE: #149 #146 * Move to fetchNASIS tests (skip on remote) * Add skip() and better handling of missing DB/no data * Use local_NASIS_defined everywhere w/ odbc::odbcListDataSources * cherry-pick: make a proper interface to sqlite NASIS queries cherry-pick: 🧬 Stitch SQLite data source API up to fetchNASIS cherry-pick: Update demo cherry-pick: Default code use 25cm, as proposed Validate/fix NASIS methods * Change name of path argument * fetchNASIS: Remove RIGHT JOIN in geomorphic features query and turn off the MSSQL specific syntax used for `d.rf.data.v2` * Method for cloning local NASIS tables into static SQLite file (#154) * Method for cloning local NASIS tables into static SQLite file #149 * local_NASIS_defined: add static_path arg and use RSQLite::dbCanConnect * Add selected set and static path to getHzErrorsNASIS * get_cosoilmoist / get_vegplot should use selected set argument * Special handling for local_NASIS_defined (does not take SS arg) * Add static_path to local_NASIS_defined * Roxygen: markdown = TRUE Broken docs md-doc: Fix single bracket semantics * Update docs * forgot to commit this one * NEWS / version 2.6.x * Rd2roxygen initial conversion; old in ./manbak * fix \href{} * passing check_man * Rd2roxygen (#162) * Rd2roxygen initial conversion; old in ./manbak * fix \href{} * passing check_man * fixes for R CMD check * deprecate old manpages * Revert existing roxygen back to human-made * get_extended_data_from_NASIS_db: artifact data query should respect SS=FALSE * get extended NASIS photo text notes: check for paths >260 chars * proper sequence to get SQLite pedon snapshot fetchNASIS-ready * Use checkHzDepthLogic (fast=TRUE) in fetchNASIS_pedons * .fetchNASIS_pedons: Use data.table for extended data processing * get_extended_data_from_NASIS_db: Replace plyr::join * dbQueryNASIS: vectorize/test; dbConnectNASIS: add NASIS() alias * docs * Add test for local NASIS DBI issues * Fix for get_cosoilmoist_from_NASISWebReport example * Fix for list output of createStaticNASIS * Close RODBC connection used in tests * Testing some pedon_table_column checks @jskovlin * aqp::union has been removed from namespace * test-fetchKSSL: hide txtProgressBar when running tests * Refactoring utils.R for data.table in fetchNASIS flattening * Docs * Oops DBI/odbc/RSQLite back in Imports * Missing comma * Docs * Mopping up * Move driver packages (odbc, RSQLite) to Suggests * get_cotext_from_NASIS_db: Add support for static_path argument and use dbQueryNASIS * get_cotext_from_NASIS_db: check for try-error * .formatParentMaterialString: Return NA_character_ for conformal data.frame with NULL data * Remove dangling require RODBC * fetchNASIS: extended data flattening handle NULL table contents * createStaticNASIS: better default arguments * Fixes for selected set argument (found by drop all _View_1 tables in a static DB) * Updates to nasisDBI "demo" that runs all the NASIS methods by all the methods * Remove requireNamespace("RODBC")--merge artifact? * demo createStaticNASIS workflow * Add WCS/SDA viz to demo * Fix bug in decoding of horizon data; thanks @dylanbeaudette * Pass through static_path argument to uncode() * Fix get_comonth_from_NASIS_db fill=TRUE * Update demos * Small adjustments to default args for demo/comparisons * Rename static_path arg to dsn * Rename static_path arg to dsn (docs) * Version bump + update README * Update NEWS.md

Method for cloning local NASIS tables into static SQLite file #149

2a35f12

brownag force-pushed the nasisSTATIC branch from e793c24 to 2a35f12 Compare January 7, 2021 01:18

brownag added the NASIS-local This tag is used for pull requests, issues, discussions etc. for soilDB local NASIS functions label Jan 7, 2021

brownag added 4 commits January 7, 2021 09:22

local_NASIS_defined: add static_path arg and use RSQLite::dbCanConnect

b04f153

Add selected set and static path to getHzErrorsNASIS

dfd040e

get_cosoilmoist / get_vegplot should use selected set argument

ec55461

Special handling for local_NASIS_defined (does not take SS arg)

e82d11b

brownag mentioned this pull request Jan 11, 2021

CRAN Release 2.5.9 #155

Closed

8 tasks

Add static_path to local_NASIS_defined

f83ce2d

brownag marked this pull request as ready for review January 29, 2021 00:06

brownag merged commit 61c56df into nasisDBI Jan 29, 2021

brownag deleted the nasisSTATIC branch January 29, 2021 00:09

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Method for cloning local NASIS tables into static SQLite file #154

Method for cloning local NASIS tables into static SQLite file #154

brownag commented Jan 7, 2021 •

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brownag commented Jan 7, 2021

Method for cloning local NASIS tables into static SQLite file #154

Method for cloning local NASIS tables into static SQLite file #154

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brownag commented Jan 7, 2021 • edited Loading

brownag commented Jan 7, 2021

brownag commented Jan 7, 2021 •

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