* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck’ * using R Under development (unstable) (2024-09-18 r87177) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RadEro/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RadEro’ version ‘1.0.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Arturo Catala ’ New submission No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Arturo", family = "Catala", role = c("aut", "cre"), email = "acatalae@gmail.com"), person(given = "Borja", family = "Latorre", role = "aut"), person(given = "Leticia", family = "Gaspar", role = "aut"), person(given = "Ana", family = "Navas", role = "aut")) as necessary. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... WARNING Subdirectory ‘RadEro/src’ contains apparent object files/libraries radimod.dll Object files/libraries should not be included in a source package. Subdirectory ‘src’ contains: radimod.dll These are unlikely file names for src files. * checking if there is a namespace ... OK * checking for executable files ... WARNING Found the following executable file: src/radimod.dll Source packages should not contain undeclared executable files. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RadEro’ can be installed ... [8s/8s] WARNING Found the following significant warnings: ./cJSON.h:83:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./cJSON.h:86:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./cJSON.h:87:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./cJSON.h:88:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./cJSON.h:92:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./cJSON.h:93:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:37:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:73:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:502:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:503:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:504:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:508:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] cJSON.c:509:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./defs.h:34:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] model.c:38:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] See ‘/srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck/00install.out’ for details. * used C compiler: ‘Debian clang version 18.1.8 (11)’ * used C++ compiler: ‘Debian clang version 18.1.8 (11)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Dependence on R version ‘4.3.1’ not with patchlevel 0 * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘RadEro.Rproj’ * 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 ... [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 ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘dplyr’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [6s/6s] NOTE RadEro_run: no visible global function definition for ‘read.table’ RadEro_run: no visible global function definition for ‘write.table’ plot: no visible global function definition for ‘read.table’ plot: no visible global function definition for ‘tail’ plot: no visible global function definition for ‘stepfun’ plot: no visible global function definition for ‘head’ plot: no visible binding for global variable ‘x’ plot: no visible binding for global variable ‘y’ plot: no visible binding for global variable ‘depth1’ plot: no visible binding for global variable ‘num2’ plot: no visible binding for global variable ‘midPROF’ plot: no visible binding for global variable ‘invCS’ resample_config: no visible global function definition for ‘tail’ resample_data: no visible global function definition for ‘tail’ resample_data: no visible global function definition for ‘head’ resample_data: no visible global function definition for ‘write.table’ Undefined global functions or variables: depth1 head invCS midPROF num2 read.table stepfun tail write.table x y Consider adding importFrom("stats", "stepfun") importFrom("utils", "head", "read.table", "tail", "write.table") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘input-data_example’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'plot.Rd' ‘data1’ ‘data2’ ‘dir1’ ‘dir2’ ‘AxisMaxValue’ ‘cell_value’ Undocumented arguments in Rd file 'resample_config.Rd' ‘data2’ ‘config1’ ‘dir1’ Undocumented arguments in Rd file 'resample_data.Rd' ‘data2’ ‘dir1’ 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 Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... WARNING Files not of a type allowed in a ‘data’ directory: ‘input-config_example.js’ Please use e.g. ‘inst/extdata’ for non-R data files * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... WARNING File ‘RadEro/libs/RadEro.so’: Found ‘__vprintf_chk’, possibly from ‘vprintf’ (C) Object: ‘model.o’ Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C) Objects: ‘cJSON.o’, ‘model.o’ Found ‘stderr’, possibly from ‘stderr’ (C) Object: ‘model.o’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking examples ... [1s/1s] ERROR Running examples in ‘RadEro-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: RadEro > ### Title: RadEro: Physically Based Compartmental Model for 137Cs Analysis > ### and Soil Redistribution Rates Estimation > ### Aliases: RadEro-package RadEro > ### Keywords: internal > > ### ** Examples > > # Example workflow for running the RadEro model: > > # Step 1: Define your working directory > directory <- getwd() # You can change this to any other directory if needed > > # Step 2: Copy example files (.csv and .js) from the package to the working directory > RadEro_example(directory) Copied: input-data_example.csv to /srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck Copied: input-config_example.js to /srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck > # Those files can be used as templates for your own projects. > > # Step 3: Execute the model with the example files > RadEro_run(data = "archivo_ejemplo.csv", config = "archivo_ejemplo.js") Starting RadEro_run... Current directory: /srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck Error in fread(file.path(dir2, data), sep = ";", header = TRUE) : File '/srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck/archivo_ejemplo.csv' does not exist or is non-readable. getwd()=='/srv/hornik/tmp/CRAN_pretest/RadEro.Rcheck' Calls: RadEro_run -> fread -> stopf -> raise_condition -> signal Execution halted * checking PDF version of manual ... [3s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘input-config_example.js’ ‘input-data_example.csv’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 8 WARNINGs, 5 NOTEs