* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pmparser.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/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 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 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/pmparser-00install.html' 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 ... [9s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [5s/67s] ERROR
  Running ‘testthat.R’ [5s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  [ 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 ──
  <COULDNT_RESOLVE_HOST/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)`: Could not resolve host: ftp.ncbi.nlm.nih.gov
  Backtrace:
      â–†
   1. ├─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:3
   2. │ └─pmparser:::getReadme(con = con)
   3. │   └─RCurl::getURL(glue("{remoteDir}/{filename}"))
   4. │     └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   5. └─RCurl (local) `<fn>`(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)
  ── Error ('test_modify_pubmed_db_dup.R:67:3'): modifyPubmedDb update is unique ──
  Error in `{
      dNow = getRemoteFilenames(glue("{remoteDir}/{subDir}/"), 
          pattern)
      dNow[, `:=`(sub_dir, subDir)]
  }`: task 1 failed - "Could not resolve host: ftp.ncbi.nlm.nih.gov"
  Backtrace:
      â–†
   1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:3
   2.   └─pmparser:::getPubmedFileInfo(localDir, subDirs = subDir, con = conTmp)
   3.     └─foreach(subDir = subDirs, .combine = rbind) %do% ...
   4.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  ── Error ('test_modify_pubmed_db_std.R:22:3'): modifyPubmedDb create matches standard ──
  <COULDNT_RESOLVE_HOST/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)`: Could not resolve host: ftp.ncbi.nlm.nih.gov
  Backtrace:
      â–†
   1. ├─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:3
   2. │ └─pmparser:::getReadme(con = con)
   3. │   └─RCurl::getURL(glue("{remoteDir}/{filename}"))
   4. │     └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   5. └─RCurl (local) `<fn>`(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov", TRUE)
  ── Error ('test_modify_pubmed_db_std.R:42:3'): modifyPubmedDb update matches standard ──
  Error in `{
      dNow = getRemoteFilenames(glue("{remoteDir}/{subDir}/"), 
          pattern)
      dNow[, `:=`(sub_dir, subDir)]
  }`: task 1 failed - "Could not resolve host: ftp.ncbi.nlm.nih.gov"
  Backtrace:
      â–†
   1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:3
   2.   └─pmparser:::getPubmedFileInfo(localDir, subDirs = subDir, con = conTmp)
   3.     └─foreach(subDir = subDirs, .combine = rbind) %do% ...
   4.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  [ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
  Error: Test failures
  In addition: 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 ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR