* using log directory ‘/srv/hornik/tmp/CRAN/PubChemR.Rcheck’ * using R Under development (unstable) (2023-12-09 r85665) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘PubChemR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PubChemR’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] Note_to_CRAN_maintainers Maintainer: ‘Selcuk Korkmaz ’ * 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 serialization versions ... OK * checking whether package ‘PubChemR’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... 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 R 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s/5s] OK * 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [3s/8s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [3s/24s] ERROR Running ‘testthat.R’ [3s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(PubChemR) > > test_check("PubChemR") The file has been saved to '/tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q/aspirin.json' The file has been saved to '/tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q/aspirin.json' The file has been saved to '/tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q/aspirin.json' The file has been saved to '/tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q/aspirin.json' The file has been saved to '/tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q/aspirin.sdf' An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (404) Not Found An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (400) Bad Request An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (404) Not Found An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Server error: (503) Service Unavailable Error in names(compounds) <- paste0("'", identifier, "'") : 'names' attribute [1] must be the same length as the vector [0] An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (400) Bad Request trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /tmp/RtmpURYVNE/working_dir/RtmpCcSI4Q Completed options trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /tmp/RtmpURYVNE/working_dir/RtmpqijM2x Completed options An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (404) Not Found Error in sidsList[[i]][[j]]$CID : $ operator is invalid for atomic vectors An error occurred: error in evaluating the argument 'content' in selecting a method for function 'fromJSON': HTTP error Client error: (404) Not Found [ FAIL 2 | WARN 0 | SKIP 0 | PASS 133 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_compounds.R:13:3'): pulling compounds via 'name' is succesfull ── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_compounds.R:14:3'): pulling compounds via 'name' is succesfull ── inherits(tmp, "list") is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 0 | SKIP 0 | PASS 133 ] Error: Test failures Execution halted * 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