* using log directory ‘/srv/hornik/tmp/CRAN_pretest/FluxSeparator.Rcheck’ * using R Under development (unstable) (2025-04-21 r88169) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘FluxSeparator/DESCRIPTION’ ... OK * this is package ‘FluxSeparator’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/7s] NOTE Maintainer: ‘Jonas Stage Sø ’ New submission Possibly misspelled words in DESCRIPTION: Ebullitive (2:52) FluxSeparator (2:8) ebullitive (12:42) Unknown, possibly misspelled, fields in DESCRIPTION: ‘DOI’ ‘Github’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid DOIs: DOI: https://doi.org/10.5281/zenodo.8297154 From: inst/CITATION Status: 404 Message: Not Found The Title field starts with the package name. * 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 ‘FluxSeparator’ can be installed ... [5s/5s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives persons with duplicated ORCID identifiers: https://orcid.org/0000-0002-9760-2571 * 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 ... WARNING Found the following file with non-ASCII characters: R/ignored.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] 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 ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘tidyverse’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s/2s] NOTE diffusive_flux: no visible global function definition for ‘%>%’ diffusive_flux: no visible global function definition for ‘drop_na’ diffusive_flux: no visible global function definition for ‘group_by’ diffusive_flux: no visible binding for global variable ‘PumpCycle’ diffusive_flux: no visible global function definition for ‘rename’ diffusive_flux: no visible global function definition for ‘any_of’ diffusive_flux: no visible global function definition for ‘add_tally’ diffusive_flux: no visible global function definition for ‘filter’ diffusive_flux: no visible binding for global variable ‘obs_in_PumpCycle’ diffusive_flux: no visible global function definition for ‘mutate’ diffusive_flux: no visible global function definition for ‘runMean’ diffusive_flux: no visible binding for global variable ‘concentration_raw’ diffusive_flux: no visible binding for global variable ‘concentration_smooth’ diffusive_flux: no visible global function definition for ‘contains’ diffusive_flux: no visible global function definition for ‘str_detect’ diffusive_flux: no visible global function definition for ‘add_count’ diffusive_flux: no visible binding for global variable ‘n’ diffusive_flux: no visible binding for global variable ‘concentration’ diffusive_flux: no visible global function definition for ‘runVar’ diffusive_flux: no visible global function definition for ‘ungroup’ diffusive_flux: no visible global function definition for ‘row_number’ diffusive_flux: no visible binding for '<<-' assignment to ‘running_var_diff’ diffusive_flux: no visible binding for global variable ‘.’ diffusive_flux: no visible binding for global variable ‘run_var5’ diffusive_flux: no visible binding for global variable ‘datetime’ diffusive_flux: no visible global function definition for ‘lag’ diffusive_flux: no visible binding for global variable ‘time_diff’ diffusive_flux: no visible binding for global variable ‘gruppering’ diffusive_flux: no visible global function definition for ‘pull’ diffusive_flux: no visible global function definition for ‘map’ diffusive_flux: no visible binding for global variable ‘running_var_diff’ diffusive_flux: no visible global function definition for ‘arrange’ diffusive_flux: no visible binding for '<<-' assignment to ‘bubbles_diff’ diffusive_flux: no visible global function definition for ‘first’ diffusive_flux: no visible global function definition for ‘if_else’ diffusive_flux: no visible binding for global variable ‘first’ diffusive_flux: no visible binding for global variable ‘min_grp’ diffusive_flux: no visible global function definition for ‘between’ diffusive_flux: no visible binding for '<<-' assignment to ‘dif_check’ diffusive_flux: no visible global function definition for ‘nest’ diffusive_flux: no visible binding for global variable ‘model’ diffusive_flux: no visible binding for global variable ‘tidy’ diffusive_flux: no visible global function definition for ‘unnest’ diffusive_flux: no visible binding for global variable ‘term’ diffusive_flux: no visible global function definition for ‘map_dbl’ diffusive_flux: no visible global function definition for ‘map_df’ diffusive_flux: no visible binding for global variable ‘tally’ diffusive_flux: no visible binding for global variable ‘model_summary’ diffusive_flux: no visible global function definition for ‘as_datetime’ diffusive_flux: no visible binding for global variable ‘datetime_start’ diffusive_flux: no visible binding for global variable ‘datetime_end’ diffusive_flux: no visible binding for global variable ‘start_value’ diffusive_flux: no visible binding for global variable ‘n_obs_included_in_lm’ diffusive_flux: no visible binding for global variable ‘estimate’ diffusive_flux: no visible binding for global variable ‘std.error’ diffusive_flux: no visible global function definition for ‘select’ diffusive_flux: no visible binding for global variable ‘slope_concentration_hr’ diffusive_flux: no visible binding for global variable ‘slope_standard_error’ diffusive_flux: no visible binding for global variable ‘p.value’ diffusive_flux: no visible binding for global variable ‘temp’ diffusive_flux: no visible binding for global variable ‘r2’ diffusive_flux: no visible binding for global variable ‘id’ diffusive_flux: no visible binding for global variable ‘time’ diffusive_flux: no visible global function definition for ‘write_csv’ diffusive_flux: no visible global function definition for ‘HMR’ diffusive_flux: no visible global function definition for ‘tibble’ diffusive_flux: no visible global function definition for ‘separate’ diffusive_flux: no visible binding for global variable ‘Series’ diffusive_flux: no visible global function definition for ‘across’ diffusive_flux: no visible binding for global variable ‘f0’ diffusive_flux: no visible binding for global variable ‘f0.up95’ diffusive_flux: no visible global function definition for ‘parse_number’ diffusive_flux: no visible binding for global variable ‘Method’ diffusive_flux: no visible binding for global variable ‘f0.se’ diffusive_flux: no visible binding for global variable ‘f0.p’ diffusive_flux: no visible binding for global variable ‘f0.lo95’ diffusive_flux: no visible binding for global variable ‘method’ diffusive_flux: no visible global function definition for ‘left_join’ diffusive_flux: no visible global function definition for ‘join_by’ diffusive_flux: no visible binding for global variable ‘hmr_slope’ diffusive_flux: no visible binding for global variable ‘dif_check’ diffusive_flux: no visible binding for global variable ‘plot_number’ diffusive_flux: no visible global function definition for ‘par’ diffusive_flux: no visible global function definition for ‘ggplot’ diffusive_flux: no visible global function definition for ‘geom_point’ diffusive_flux: no visible global function definition for ‘aes’ diffusive_flux: no visible global function definition for ‘geom_smooth’ diffusive_flux: no visible global function definition for ‘scale_color_gradient’ diffusive_flux: no visible global function definition for ‘labs’ diffusive_flux: no visible global function definition for ‘guides’ diffusive_flux: no visible global function definition for ‘guide_colourbar’ diffusive_flux: no visible global function definition for ‘scale_x_datetime’ diffusive_flux: no visible global function definition for ‘theme’ ebullitive_flux: no visible global function definition for ‘par’ ebullitive_flux: no visible global function definition for ‘%>%’ ebullitive_flux: no visible global function definition for ‘drop_na’ ebullitive_flux: no visible global function definition for ‘group_by’ ebullitive_flux: no visible binding for global variable ‘PumpCycle’ ebullitive_flux: no visible binding for global variable ‘sensor’ ebullitive_flux: no visible global function definition for ‘rename’ ebullitive_flux: no visible global function definition for ‘any_of’ ebullitive_flux: no visible global function definition for ‘add_tally’ ebullitive_flux: no visible global function definition for ‘filter’ ebullitive_flux: no visible binding for global variable ‘obs_in_PumpCycle’ ebullitive_flux: no visible global function definition for ‘mutate’ ebullitive_flux: no visible global function definition for ‘runMean’ ebullitive_flux: no visible binding for global variable ‘concentration_raw’ ebullitive_flux: no visible binding for global variable ‘concentration_smooth’ ebullitive_flux: no visible global function definition for ‘contains’ ebullitive_flux: no visible global function definition for ‘str_detect’ ebullitive_flux: no visible global function definition for ‘reframe’ ebullitive_flux: no visible binding for global variable ‘datetime’ ebullitive_flux: no visible global function definition for ‘add_count’ ebullitive_flux: no visible binding for global variable ‘n’ ebullitive_flux: no visible binding for global variable ‘concentration’ ebullitive_flux: no visible global function definition for ‘runVar’ ebullitive_flux: no visible global function definition for ‘ungroup’ ebullitive_flux: no visible global function definition for ‘row_number’ ebullitive_flux: no visible binding for global variable ‘run_var5’ ebullitive_flux: no visible global function definition for ‘lag’ ebullitive_flux: no visible binding for global variable ‘time_diff’ ebullitive_flux: no visible binding for global variable ‘gruppering’ ebullitive_flux: no visible global function definition for ‘pull’ ebullitive_flux: no visible global function definition for ‘map’ ebullitive_flux: no visible binding for global variable ‘PumpCycle_Timediff’ ebullitive_flux: no visible global function definition for ‘summarise’ ebullitive_flux: no visible binding for global variable ‘tempC’ ebullitive_flux: no visible binding for global variable ‘PumpCycle_Timediff_hr’ ebullitive_flux: no visible global function definition for ‘select’ ebullitive_flux: no visible global function definition for ‘first’ ebullitive_flux: no visible global function definition for ‘last’ ebullitive_flux: no visible global function definition for ‘if_else’ ebullitive_flux: no visible binding for global variable ‘first’ ebullitive_flux: no visible binding for global variable ‘last’ ebullitive_flux: no visible global function definition for ‘bind_rows’ ebullitive_flux: no visible global function definition for ‘arrange’ ebullitive_flux: no visible global function definition for ‘summarize’ ebullitive_flux: no visible binding for global variable ‘top_concentration’ ebullitive_flux: no visible binding for global variable ‘min_concentration’ ebullitive_flux: no visible binding for global variable ‘concentration_diff’ ebullitive_flux: no visible binding for global variable ‘min_datetime’ ebullitive_flux: no visible binding for global variable ‘max_datetime’ ebullitive_flux: no visible binding for global variable ‘sum_bobler’ ebullitive_flux: no visible binding for global variable ‘n_bobler’ ebullitive_flux: no visible binding for global variable ‘time’ ebullitive_flux: no visible binding for global variable ‘temp’ ebullitive_flux: no visible binding for global variable ‘n_bubbles’ ebullitive_flux: no visible binding for global variable ‘pumpcycle_duration_hr’ ebullitive_flux: no visible binding for global variable ‘sum_bubbles_concentration’ ebullitive_flux: no visible global function definition for ‘full_join’ ebullitive_flux: no visible binding for global variable ‘datetime_start’ ebullitive_flux: no visible binding for global variable ‘datetime_end’ ebullitive_flux: no visible binding for global variable ‘concentration_per_time’ ebullitive_flux: no visible binding for global variable ‘ungroup’ ebullitive_flux: no visible binding for global variable ‘plot_number’ ebullitive_flux: no visible global function definition for ‘ggplot’ ebullitive_flux: no visible global function definition for ‘aes’ ebullitive_flux: no visible global function definition for ‘geom_point’ ebullitive_flux: no visible global function definition for ‘geom_vline’ ebullitive_flux: no visible binding for global variable ‘datetime_bubbles’ ebullitive_flux: no visible global function definition for ‘scale_x_datetime’ ebullitive_flux: no visible global function definition for ‘scale_y_continuous’ ebullitive_flux: no visible global function definition for ‘labs’ ebullitive_flux: no visible global function definition for ‘scale_color_manual’ ebullitive_flux: no visible global function definition for ‘geom_hline’ ebullitive_flux: no visible global function definition for ‘theme’ ebullitive_flux: no visible global function definition for ‘ggarrange’ read_CH4_files: no visible binding for global variable ‘model_coef’ read_CH4_files: no visible global function definition for ‘%>%’ read_CH4_files: no visible global function definition for ‘inner_join’ read_CH4_files: no visible global function definition for ‘rename’ read_CH4_files: no visible binding for global variable ‘path’ read_CH4_files: no visible global function definition for ‘mutate’ read_CH4_files: no visible binding for global variable ‘read_csv’ read_CH4_files: no visible global function definition for ‘col_double’ read_CH4_files: no visible global function definition for ‘col_character’ read_CH4_files: no visible global function definition for ‘unnest’ read_CH4_files: no visible global function definition for ‘any_of’ read_CH4_files: no visible global function definition for ‘ymd_hms’ read_CH4_files: no visible binding for global variable ‘datetime’ read_CH4_files: no visible binding for global variable ‘tempC’ read_CH4_files: no visible binding for global variable ‘RH’ read_CH4_files: no visible binding for global variable ‘abs_H’ read_CH4_files: no visible binding for global variable ‘g’ read_CH4_files: no visible binding for global variable ‘S’ read_CH4_files: no visible binding for global variable ‘CH4smV’ read_CH4_files: no visible binding for global variable ‘V0’ read_CH4_files: no visible binding for global variable ‘a’ read_CH4_files: no visible binding for global variable ‘RsR0’ read_CH4_files: no visible binding for global variable ‘b’ read_CH4_files: no visible binding for global variable ‘K’ read_CH4_files: no visible global function definition for ‘select’ read_CH4_files: no visible binding for global variable ‘K33_RH’ read_CH4_files: no visible binding for global variable ‘.’ read_CH4_files: no visible binding for global variable ‘pred_CH4’ read_CH4_files: no visible binding for global variable ‘sensor’ read_CH4_files: no visible global function definition for ‘contains’ Undefined global functions or variables: %>% . CH4smV HMR K K33_RH Method PumpCycle PumpCycle_Timediff PumpCycle_Timediff_hr RH RsR0 S Series V0 a abs_H across add_count add_tally aes any_of arrange as_datetime b between bind_rows col_character col_double concentration concentration_diff concentration_per_time concentration_raw concentration_smooth contains datetime datetime_bubbles datetime_end datetime_start dif_check drop_na estimate f0 f0.lo95 f0.p f0.se f0.up95 filter first full_join g geom_hline geom_point geom_smooth geom_vline ggarrange ggplot group_by gruppering guide_colourbar guides hmr_slope id if_else inner_join join_by labs lag last left_join map map_dbl map_df max_datetime method min_concentration min_datetime min_grp model model_coef model_summary mutate n n_bobler n_bubbles n_obs_included_in_lm nest obs_in_PumpCycle p.value par parse_number path plot_number pred_CH4 pull pumpcycle_duration_hr r2 read_csv reframe rename row_number runMean runVar run_var5 running_var_diff scale_color_gradient scale_color_manual scale_x_datetime scale_y_continuous select sensor separate slope_concentration_hr slope_standard_error start_value std.error str_detect sum_bobler sum_bubbles_concentration summarise summarize tally temp tempC term theme tibble tidy time time_diff top_concentration ungroup unnest write_csv ymd_hms Consider adding importFrom("graphics", "par") importFrom("stats", "filter", "lag", "time") to your NAMESPACE file. * checking Rd files ... [0s/0s] NOTE prepare_Rd: Diffusive_flux.Rd:82-84: Dropping empty section \seealso prepare_Rd: Ebullitive_flux.Rd:58-60: Dropping empty section \note prepare_Rd: Ebullitive_flux.Rd:64-66: Dropping empty section \seealso prepare_Rd: ppm_to_umol.Rd:19-21: Dropping empty section \details prepare_Rd: ppm_to_umol.Rd:22-28: Dropping empty section \value prepare_Rd: ppm_to_umol.Rd:37-39: Dropping empty section \note prepare_Rd: ppm_to_umol.Rd:43-45: Dropping empty section \seealso prepare_Rd: read_CH4_files.Rd:37-39: Dropping empty section \note prepare_Rd: read_CH4_files.Rd:43-45: Dropping empty section \seealso * 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 R/sysdata.rda ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘FluxSeparator-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: diffusive_flux > ### Title: diffusive_flux > ### Aliases: diffusive_flux > > ### ** Examples > > library(FluxSeparator) > > # Load dataset > DIY_sensor_data <- data(DIY_sensor_data) > > DIY_sensor_data [1] "DIY_sensor_data" > diffusive_flux() Error in diffusive_flux() : could not find function "diffusive_flux" Execution halted * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] NOTE Found the following HTML validation problems: DIY_sensor_data.html:38:1 (DIY_sensor_data.Rd:8): Warning: trimming empty

* checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 6 NOTEs