* using log directory ‘/srv/hornik/tmp/CRAN/clintrialx.Rcheck’ * using R Under development (unstable) (2024-08-20 r87029) * 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 ‘clintrialx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘clintrialx’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/8s] NOTE Maintainer: ‘Indraneel Chakraborty ’ New submission Possibly misspelled words in DESCRIPTION: AACT (8:318) CTTI (8:313) ClinicalTrials (8:286) clintrialx (8:229) Found the following (possibly) invalid URLs: URL: http://ineelhere.github.io/clintrialx/ (moved to https://www.indraneelchakraborty.com/clintrialx/) From: DESCRIPTION Status: 301 Message: Moved Permanently URL: https://github.com/ineelhere/clintrialx/blob/main/CONTRIBUTING.md From: README.md Status: 404 Message: Not Found URL: https://ineelhere.github.io/clintrialx (moved to https://www.indraneelchakraborty.com/clintrialx/) From: man/ctg_data_report.Rd Status: 301 Message: Moved Permanently URL: https://ineelhere.github.io/clintrialx/ (moved to https://www.indraneelchakraborty.com/clintrialx/) From: README.md Status: 301 Message: Moved Permanently URL: https://ineelhere.github.io/clintrialx/report.html (moved to https://www.indraneelchakraborty.com/clintrialx/report.html) From: man/ctg_data_report.Rd README.md Status: 301 Message: Moved Permanently URL: https://opensource.org/licenses/Apache-2.0 (moved to https://opensource.org/license/apache-2-0) 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: ‘Connect and work with clinical trials data sources with R programming.’ In title case that is: ‘Connect and Work with Clinical Trials Data Sources with R Programming.’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'httr', 'lubridate', 'readr', 'dplyr', 'progress', 'RPostgreSQL' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘clintrialx’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: ‘CODE_OF_CONDUCT.md’ ‘logo.png’ * 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 files with non-ASCII characters: R/ctg_bulk_fetch.R R/hello.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 ... WARNING '::' or ':::' import not declared from: ‘tibble’ Packages in Depends field not imported from: ‘RPostgreSQL’ ‘dplyr’ ‘httr’ ‘lubridate’ ‘progress’ ‘readr’ 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 aact_check_connection: no visible global function definition for ‘dbGetQuery’ aact_connection: no visible global function definition for ‘dbConnect’ aact_connection: no visible global function definition for ‘dbDriver’ aact_custom_query: no visible global function definition for ‘dbGetQuery’ ctg_count: no visible global function definition for ‘headers’ ctg_data_report : is_installed: no visible global function definition for ‘installed.packages’ ctg_data_report: no visible global function definition for ‘install.packages’ ctg_data_report : get_colors: no visible global function definition for ‘colorRampPalette’ ctg_data_report: no visible global function definition for ‘render’ ctg_get_fields: no visible global function definition for ‘headers’ Undefined global functions or variables: colorRampPalette dbConnect dbDriver dbGetQuery headers install.packages installed.packages render Consider adding importFrom("grDevices", "colorRampPalette") importFrom("utils", "install.packages", "installed.packages") to your NAMESPACE file. * checking Rd files ... [0s/0s] NOTE checkRd: (-1) ctg_data_report.Rd:66: Lost braces 66 | Click here for an example report - \url{https://ineelhere.github.io/clintrialx/report.html}{report.html}. | ^ * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘build_query_params’ ‘create_progress_bar’ ‘fetch_all_pages’ ‘fetch_data’ ‘get_total_count’ ‘validate_status’ 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘usecase-doc.Rmd’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... [1s/2s] ERROR Running examples in ‘clintrialx-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: aact_check_connection > ### Title: Check database connection > ### Aliases: aact_check_connection > > ### ** Examples > > # Set environment variables for database credentials in .Renviron and load it > # readRenviron(".Renviron") > > # Connect to the database > con <- aact_connection(Sys.getenv('user'), Sys.getenv('password')) Error in postgresqlNewConnection(drv, ...) : RPosgreSQL error: could not connect hornik@aact-db.ctti-clinicaltrials.org:5432 on dbname "aact": connection to server at "aact-db.ctti-clinicaltrials.org" (174.138.61.222), port 5432 failed: fe_sendauth: no password supplied Calls: aact_connection -> dbConnect -> dbConnect -> postgresqlNewConnection Execution halted * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 WARNINGs, 7 NOTEs