• using R Under development (unstable) (2025-12-07 r89119)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.6 (2)     Debian flang version 21.1.6 (2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘pmparser/DESCRIPTION’ ... OK
• this is package ‘pmparser’ version ‘1.0.21’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] OK
• 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 ‘pmparser’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... 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 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 ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/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 ... [10s/15s] OK
• checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [6s/12s] ERROR   Running ‘testthat.R’ [6s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(pmparser)   >   > test_check('pmparser')   Saving _problems/test_modify_pubmed_db_dup-53.R   Saving _problems/test_modify_pubmed_db_dup-69.R   Saving _problems/test_modify_pubmed_db_std-24.R   Saving _problems/test_modify_pubmed_db_std-44.R   [ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]      ══ Skipped tests (4) ═══════════════════════════════════════════════════════════   • On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',     'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_modify_pubmed_db_dup.R:51:3'): modifyPubmedDb create is unique ──   Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero   Backtrace:       ▆    1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:3    2. └─pmparser::getCitation(...)   ── Error ('test_modify_pubmed_db_dup.R:67:3'): modifyPubmedDb update is unique ──   Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero   Backtrace:       ▆    1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:3    2. └─pmparser::getCitation(...)   ── Error ('test_modify_pubmed_db_std.R:22:3'): modifyPubmedDb create matches standard ──   Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero   Backtrace:       ▆    1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:3    2. └─pmparser::getCitation(...)   ── Error ('test_modify_pubmed_db_std.R:42:3'): modifyPubmedDb update matches standard ──   Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero   Backtrace:       ▆    1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:3    2. └─pmparser::getCitation(...)      [ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]   Error:   ! Test failures.   Warning message:   call dbDisconnect() when finished working with a connection   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [1s/2s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR