* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ambrosia.Rcheck’ * using R Under development (unstable) (2025-03-24 r88048) * 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 ‘ambrosia/DESCRIPTION’ ... OK * this is package ‘ambrosia’ version ‘2.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Kanishka Narayan ’ New submission Non-FOSS package license (BSD2) Possibly misspelled words in DESCRIPTION: Edmonds (10:254) al (10:265) et (10:262) Reading CITATION file fails with 2:1: unexpected '@' 1: 2: @ ^ when package is not installed. Found the following (possibly) invalid URLs: URL: http://www.globalchange.umd.edu/gcam/ (moved to http://www.pnnl.gov/projects/jgcri/gcam/) From: README.md Status: 301 Message: Moved Permanently URL: https://codecov.io/gh/JGCRI/ambrosia (moved to https://app.codecov.io/gh/JGCRI/ambrosia) From: README.md Status: 301 Message: Moved Permanently URL: https://joss.theoj.org/papers/b1af4bb026f674b31d1175075607deef (moved to https://joss.theoj.org/papers/10.21105/joss.02890) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘An R package for calculating and analyzing food demand that is responsive to changing incomes and prices’ In title case that is: ‘An R Package for Calculating and Analyzing Food Demand that is Responsive to Changing Incomes and Prices’ * 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 ... NOTE Found the following hidden files and directories: .github These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about .github * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ambrosia’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: BSD2 Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: ‘DISCLAIMER’ ‘paper’ ‘scripts’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in parse(con): 2:1: unexpected '@' 1: 2: @ ^ * 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) create_dataset_for_parameter_fit.Rd:28: Lost braces; missing escapes or markup? 28 | {s_cal_pcap_day_thous} (Containing 1000 calories per capita per day for staples) | ^ checkRd: (-1) create_dataset_for_parameter_fit.Rd:30: Lost braces; missing escapes or markup? 30 | {ns_cal_pcap_day_thous} (Containing 1000 calories per capita per day for non-staples) | ^ checkRd: (-1) create_dataset_for_parameter_fit.Rd:32: Lost braces; missing escapes or markup? 32 | {gdp_pcap_thous} (Containing GDP per capita) | ^ checkRd: (-1) create_dataset_for_parameter_fit.Rd:34: Lost braces; missing escapes or markup? 34 | {s_usd_p1000cal} (Price of 1000 calories for staples per person per day) | ^ checkRd: (-1) create_dataset_for_parameter_fit.Rd:36: Lost braces; missing escapes or markup? 36 | {ns_usd_p1000cal} (Price of 1000 calories for non-staples per person per day)} | ^ * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'calculate_ambrosia_params.Rd': ‘create_dataset_for_parameter_fit()’ Missing link(s) in Rd file 'vec2param.Rd': ‘A_s, A_n, xi_ss, xi_cross, xi_nn, nu1_n, lambda_s, k_s, Pm, psscl, pnscl’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: calculate_ambrosia_params.Rd: create_dataset_for_parameter_fit() vec2param.Rd: A_s, A_n, xi_ss, xi_cross, xi_nn, nu1_n, lambda_s, k_s, Pm, psscl, pnscl Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘data_used_for_original_param’ ‘mc_data_example’ ‘processed_data_example’ ‘training_data’ Undocumented data sets: ‘data_used_for_original_param’ ‘mc_data_example’ ‘processed_data_example’ ‘training_data’ 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 'calc1q.Rd' ‘psscl’ ‘pnscl’ ‘staples_FE’ ‘bias_adder_s’ ‘bias_adder_ns’ Undocumented arguments in Rd file 'food.dmnd.Rd' ‘staples_FE’ ‘bias_adder_s’ ‘bias_adder_ns’ 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 ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress data_used_for_original_param.RData 85Kb 75Kb xz mc_data_example.RData 17Kb 15Kb xz processed_data_example.RData 531Kb 433Kb xz training_data.RData 723Kb 628Kb xz * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: scripts/cpp/Makefile Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking include directives in Makefiles ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [38s/38s] OK Running ‘testthat.R’ [38s/38s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... NOTE Found the following files/directories: ‘RtmphjsrDaProcessed_Data_for_MC.csv’ ‘RtmphjsrDaparameter_data.csv’ * DONE Status: 7 WARNINGs, 5 NOTEs