Running 'testthat.R' [23m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed23n1167.xml.gz.md5'
  Content length 60 bytes
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed23n1167.xml.gz'
   length 69525757 bytes (66.3 MB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed23n1167.xml.gz.md5'
  Content length 60 bytes
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed23n1167.xml.gz'
   length 69525757 bytes (66.3 MB)
  ==================================================
  [ FAIL 31 | WARN 4 | SKIP 4 | PASS 98 ]
  
  == Skipped tests ===============================================================
  * On CRAN (4)
  
  == Failed tests ================================================================
  -- Error ('test_modify_pubmed_db_dup.R:51'): modifyPubmedDb create is unique ---
  Error in `gzfile(file, open = "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:2
   2.   \-pmparser::getCitation(...)
   3.     \-pmparser:::writeTableInChunks(...)
   4.       +-R.utils::countLines(path)
   5.       \-R.utils::countLines.default(path)
   6.         \-base::gzfile(file, open = "rb")
  -- Failure ('test_modify_pubmed_db_dup.R:76'): modifyPubmedDb update is unique --
  comment not equal to 0L.
  1/1 mismatches
  [1] 18 - 0 == 18
  -- Failure ('test_modify_pubmed_db_dup.R:76'): modifyPubmedDb update is unique --
  data_bank not equal to 0L.
  1/1 mismatches
  [1] 6 - 0 == 6
  -- Error ('test_modify_pubmed_db_std.R:22'): modifyPubmedDb create matches standard --
  Error in `gzfile(file, open = "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:2
   2.   \-pmparser::getCitation(...)
   3.     \-pmparser:::writeTableInChunks(...)
   4.       +-R.utils::countLines(path)
   5.       \-R.utils::countLines.default(path)
   6.         \-base::gzfile(file, open = "rb")
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (54500, 117) differ >
  Component "pmid": Numeric: lengths (54500, 117) differ
  Component "text": Lengths (54500, 117) differ (string compare on first 117)
  Component "text": 60 string mismatches
  Component "label": Lengths (54500, 117) differ (string compare on first 117)
  Component "label": 'is.NA' value mismatch: 30 in current 35 in target
  Component "nlm_category": Lengths (54500, 117) differ (string compare on first 117)
  Component "nlm_category": 'is.NA' value mismatch: 73 in current 51 in target
  Component "abstract_pos": Numeric: lengths (54500, 117) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (17890, 34) differ >
  Component "pmid": Numeric: lengths (17890, 34) differ
  Component "copyright": Lengths (17890, 34) differ (string compare on first 34)
  Component "copyright": 15 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  article not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (29991, 58) differ >
  Component "pmid": Numeric: lengths (29991, 58) differ
  Component "title": Lengths (29991, 58) differ (string compare on first 58)
  Component "title": 30 string mismatches
  Component "pub_date": Numeric: lengths (29991, 58) differ
  Component "pub_model": Lengths (29991, 58) differ (string compare on first 58)
  Component "pub_model": 19 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  article_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (36832, 76) differ >
  Component "pmid": Numeric: lengths (36832, 76) differ
  Component "id_type": Lengths (36832, 76) differ (string compare on first 76)
  Component "id_type": 17 string mismatches
  Component "id_value": Lengths (36832, 76) differ (string compare on first 76)
  Component "id_value": 38 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (185642, 386) differ >
  Component "pmid": Numeric: lengths (185642, 386) differ
  Component "author_pos": Numeric: lengths (185642, 386) differ
  Component "last_name": Lengths (185642, 386) differ (string compare on first 386)
  Component "last_name": 'is.NA' value mismatch: 5 in current 3 in target
  Component "fore_name": Lengths (185642, 386) differ (string compare on first 386)
  Component "fore_name": 'is.NA' value mismatch: 5 in current 3 in target
  Component "initials": Lengths (185642, 386) differ (string compare on first 386)
  Component "initials": 'is.NA' value mismatch: 5 in current 3 in target
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (215199, 453) differ >
  Component "pmid": Numeric: lengths (215199, 453) differ
  Component "author_pos": Numeric: lengths (215199, 453) differ
  Component "affiliation_pos": Numeric: lengths (215199, 453) differ
  Component "affiliation": Lengths (215199, 453) differ (string compare on first 453)
  Component "affiliation": 235 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (1670, 0) differ >
  Component "pmid": Numeric: lengths (1670, 0) differ
  Component "author_pos": Numeric: lengths (1670, 0) differ
  Component "affiliation_pos": Numeric: lengths (1670, 0) differ
  Component "source": Lengths (1670, 0) differ (string compare on first 0)
  Component "identifier": Lengths (1670, 0) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (34957, 60) differ >
  Component "pmid": Numeric: lengths (34957, 60) differ
  Component "author_pos": Numeric: lengths (34957, 60) differ
  Component "source": Lengths (34957, 60) differ (string compare on first 60)
  Component "identifier": Lengths (34957, 60) differ (string compare on first 60)
  Component "identifier": 42 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (27173, 58) differ >
  Component "pmid": Numeric: lengths (27173, 58) differ
  Component "complete": Lengths (27173, 58) differ (string compare on first 58)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  chemical not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (9549, 44) differ >
  Component "pmid": Numeric: lengths (9549, 44) differ
  Component "registry_number": Lengths (9549, 44) differ (string compare on first 44)
  Component "registry_number": 31 string mismatches
  Component "substance_name": Lengths (9549, 44) differ (string compare on first 44)
  Component "substance_name": 44 string mismatches
  Component "substance_ui": Lengths (9549, 44) differ (string compare on first 44)
  Component "substance_ui": 44 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  comment not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (1602, 8) differ >
  Component "pmid": Numeric: lengths (1602, 8) differ
  Component "ref_type": Lengths (1602, 8) differ (string compare on first 8)
  Component "ref_type": 3 string mismatches
  Component "ref_pmid": Numeric: lengths (1602, 8) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  data_bank not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (707, 6) differ >
  Component "pmid": Numeric: lengths (707, 6) differ
  Component "data_bank_name": Lengths (707, 6) differ (string compare on first 6)
  Component "data_bank_name": 2 string mismatches
  Component "accession_number": Lengths (707, 6) differ (string compare on first 6)
  Component "accession_number": 2 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  grant_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (15795, 34) differ >
  Component "pmid": Numeric: lengths (15795, 34) differ
  Component "grant_id": Lengths (15795, 34) differ (string compare on first 34)
  Component "grant_id": 'is.NA' value mismatch: 2 in current 0 in target
  Component "acronym": Lengths (15795, 34) differ (string compare on first 34)
  Component "acronym": 'is.NA' value mismatch: 17 in current 13 in target
  Component "agency": Lengths (15795, 34) differ (string compare on first 34)
  Component "agency": 18 string mismatches
  Component "country": Lengths (15795, 34) differ (string compare on first 34)
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  grant_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (5350, 12) differ >
  Component "pmid": Numeric: lengths (5350, 12) differ
  Component "complete": Lengths (5350, 12) differ (string compare on first 12)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  investigator not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (42552, 54) differ >
  Component "pmid": Numeric: lengths (42552, 54) differ
  Component "investigator_pos": Numeric: lengths (42552, 54) differ
  Component "last_name": Lengths (42552, 54) differ (string compare on first 54)
  Component "last_name": 27 string mismatches
  Component "fore_name": Lengths (42552, 54) differ (string compare on first 54)
  Component "fore_name": 27 string mismatches
  Component "initials": Lengths (42552, 54) differ (string compare on first 54)
  Component "initials": 25 string mismatches
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (293, 0) differ >
  Component "pmid": Numeric: lengths (293, 0) differ
  Component "investigator_pos": Numeric: lengths (293, 0) differ
  Component "affiliation_pos": Numeric: lengths (293, 0) differ
  Component "affiliation": Lengths (293, 0) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  journal not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (29991, 58) differ >
  Component "pmid": Numeric: lengths (29991, 58) differ
  Component "journal_name": Lengths (29991, 58) differ (string compare on first 58)
  Component "journal_name": 30 string mismatches
  Component "journal_iso": Lengths (29991, 58) differ (string compare on first 58)
  Component "journal_iso": 30 string mismatches
  Component "pub_date": Numeric: lengths (29991, 58) differ
  Component "pub_year": Lengths (29991, 58) differ (string compare on first 58)
  Component "pub_year": 30 string mismatches
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  keyword_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (95303, 195) differ >
  Component "pmid": Numeric: lengths (95303, 195) differ
  Component "keyword_name": Lengths (95303, 195) differ (string compare on first 195)
  Component "keyword_name": 93 string mismatches
  Component "major_topic": Lengths (95303, 195) differ (string compare on first 195)
  Component "major_topic": 56 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  keyword_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (18061, 39) differ >
  Component "pmid": Numeric: lengths (18061, 39) differ
  Component "list_owner": Lengths (18061, 39) differ (string compare on first 39)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (44103, 256) differ >
  Component "pmid": Numeric: lengths (44103, 256) differ
  Component "descriptor_pos": Lengths (44103, 256) differ (string compare on first 256)
  Component "descriptor_pos": 251 string mismatches
  Component "descriptor_name": Lengths (44103, 256) differ (string compare on first 256)
  Component "descriptor_name": 256 string mismatches
  Component "descriptor_ui": Lengths (44103, 256) differ (string compare on first 256)
  Component "descriptor_ui": 256 string mismatches
  Component "descriptor_major_topic": Lengths (44103, 256) differ (string compare on first 256)
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (5393, 13) differ >
  Component "pmid": Numeric: lengths (5393, 13) differ
  Component "indexing_method": Lengths (5393, 13) differ (string compare on first 13)
  Component "indexing_method": 5 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (18519, 152) differ >
  Component "pmid": Numeric: lengths (18519, 152) differ
  Component "descriptor_pos": Lengths (18519, 152) differ (string compare on first 152)
  Component "descriptor_pos": 142 string mismatches
  Component "qualifier_name": Lengths (18519, 152) differ (string compare on first 152)
  Component "qualifier_name": 145 string mismatches
  Component "qualifier_ui": Lengths (18519, 152) differ (string compare on first 152)
  Component "qualifier_ui": 145 string mismatches
  Component "qualifier_major_topic": Lengths (18519, 152) differ (string compare on first 152)
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  other_abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (643, 4) differ >
  Component "pmid": Numeric: lengths (643, 4) differ
  Component "text": Lengths (643, 4) differ (string compare on first 4)
  Component "text": 2 string mismatches
  Component "type": Lengths (643, 4) differ (string compare on first 4)
  Component "type": 1 string mismatch
  Component "language": Lengths (643, 4) differ (string compare on first 4)
  Component "language": 2 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  other_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (2, 0) differ >
  Component "pmid": Numeric: lengths (2, 0) differ
  Component "source": Lengths (2, 0) differ (string compare on first 0)
  Component "id_value": Lengths (2, 0) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pmid_status not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (30033, 106) differ >
  Component "pmid": Numeric: lengths (30033, 106) differ
  Component "version": Numeric: lengths (30033, 106) differ
  Component "xml_filename": Lengths (30033, 106) differ (string compare on first 106)
  Component "xml_filename": 78 string mismatches
  Component "status": Lengths (30033, 106) differ (string compare on first 106)
  Component "status": 52 string mismatches
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pub_history not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (139999, 254) differ >
  Component "pmid": Numeric: lengths (139999, 254) differ
  Component "pub_status": Lengths (139999, 254) differ (string compare on first 254)
  Component "pub_status": 98 string mismatches
  Component "pub_date": Numeric: lengths (139999, 254) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pub_type not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (37344, 79) differ >
  Component "pmid": Numeric: lengths (37344, 79) differ
  Component "type_name": Lengths (37344, 79) differ (string compare on first 79)
  Component "type_name": 38 string mismatches
  Component "type_id": Lengths (37344, 79) differ (string compare on first 79)
  Component "type_id": 38 string mismatches
  
  [ FAIL 31 | WARN 4 | SKIP 4 | PASS 98 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted