* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PhotoGEA.Rcheck’
* using R Under development (unstable) (2025-04-06 r88113)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PhotoGEA/DESCRIPTION’ ... OK
* this is package ‘PhotoGEA’ version ‘1.3.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/8s] NOTE
Maintainer: ‘Edward B. Lochocki <eloch@illinois.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Lochocki (7:5)
  McGrath (7:32)
  Salesse (7:15)
* 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 ‘PhotoGEA’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [10s/10s] OK
* checking Rd files ... [1s/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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] ERROR
Running examples in ‘PhotoGEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_gm_busch
> ### Title: Calculate mesophyll conductance to CO2 diffusion
> ### Aliases: calculate_gm_busch
> 
> ### ** Examples
> 
> ## In this example we load gas exchange and TDL data files, calibrate the TDL
> ## data, pair the data tables together, and then calculate mesophyll conductance
> 
> # Read the TDL data file, making sure to interpret the time zone as US Central
> # time
> tdl_data <- read_gasex_file(
+   PhotoGEA_example_file_path('tdl_for_gm.dat'),
+   'TIMESTAMP',
+   list(tz = 'US/Central')
+ )
> 
> # Identify cycles within the TDL data
> tdl_data <- identify_tdl_cycles(
+   tdl_data,
+   valve_column_name = 'valve_number',
+   cycle_start_valve = 20,
+   expected_cycle_length_minutes = 2.7,
+   expected_cycle_num_valves = 9,
+   timestamp_colname = 'TIMESTAMP'
+ )
> 
> # Use reference tanks to calibrate the TDL data
> processed_tdl <- consolidate(by(
+   tdl_data,
+   tdl_data[, 'cycle_num'],
+   process_tdl_cycle_erml,
+   noaa_valve = 2,
+   calibration_0_valve = 20,
+   calibration_1_valve = 21,
+   calibration_2_valve = 23,
+   calibration_3_valve = 26,
+   noaa_cylinder_co2_concentration = 294.996,
+   noaa_cylinder_isotope_ratio = -8.40,
+   calibration_isotope_ratio = -11.505
+ ))
> 
> # Read the gas exchange data, making sure to interpret the time stamp in the US
> # Central time zone
> licor_data <- read_gasex_file(
+   PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
+   'time',
+   list(tz = 'US/Central')
+ )
> 
> # Get TDL valve information from Licor file name; for this TDL system, the
> # reference valve is 12 when the sample valve is 11
> licor_data <- get_sample_valve_from_filename(licor_data, list('11' = 12))
> 
> # Get oxygen info from the Licor file preamble (needed for calculate_gamma_star)
> licor_data <- get_oxygen_from_preamble(licor_data)
> 
> # Pair the Licor and TDL data by locating the TDL cycle corresponding to each
> # Licor measurement
> licor_data <- pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data)
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:15:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 260.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:18:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 263.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:21:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 266.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:24:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 269.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:27:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 272.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:30:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 275.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:33:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 278.040000001589 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:36:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 281.041666666667 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:39:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 284.041666666667 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:42:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 287.041666666667 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:45:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 290.041666666667 minutes away, exceeding the maximum allowed value of 1 minutes
Warning in pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data) :
  Could not find a time point in the TDL data corresponding to 2023-08-04 13:48:15, a point in the Licor data.
The nearest time in the TDL data was 2023-08-04 08:55:12,
which is 293.041666666667 minutes away, exceeding the maximum allowed value of 1 minutes
> 
> # Calculate total pressure (needed for calculate_gas_properties)
> licor_data <- calculate_total_pressure(licor_data)
> 
> # Calculate Csurface (needed for calculate_ternary_correction)
> licor_data <- calculate_gas_properties(licor_data)
> 
> # Calculate ternary correction
> licor_data <- calculate_ternary_correction(licor_data)
> 
> # Set Rubisco specificity (needed for calculate_gamma_star)
> licor_data <- set_variable(
+     licor_data,
+     'rubisco_specificity_tl',
+     'M / M',
+     value = 90
+ )
> 
> # Calculate Gamma_star (needed for calculate_gm_busch)
> licor_data <- calculate_gamma_star(licor_data)
> 
> # Calculate isotope discrimination (needed for calculate_gm_busch)
> licor_data <- calculate_isotope_discrimination(licor_data)
Error in check_required_variables.data.frame(x$main_data, names(required_variables),  : 
  The following required columns are all NA: delta_C13_r, delta_C13_s, calibrated_12c_r, calibrated_12c_s
Calls: calculate_isotope_discrimination ... check_required_variables -> check_required_variables.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [67s/67s] OK
  Running ‘testthat.R’ [67s/67s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/18s] OK
* checking PDF version of manual ... [7s/7s] OK
* checking HTML version of manual ... [5s/5s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE