CRAN Package Check Results for Package dbparser

Last updated on 2019-07-15 00:50:27 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 7.30 62.53 69.83 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.3 5.87 49.81 55.68 OK
r-devel-linux-x86_64-fedora-clang 1.0.3 84.37 OK
r-devel-linux-x86_64-fedora-gcc 1.0.3 86.35 OK
r-devel-windows-ix86+x86_64 1.0.3 20.00 115.00 135.00 OK
r-patched-linux-x86_64 1.0.3 6.18 62.39 68.57 OK
r-patched-solaris-x86 1.0.3 107.40 OK
r-release-linux-x86_64 1.0.3 6.40 62.17 68.57 OK
r-release-windows-ix86+x86_64 1.0.2 13.00 89.00 102.00 OK
r-release-osx-x86_64 1.0.3 OK
r-oldrel-windows-ix86+x86_64 1.0.1 19.00 98.00 117.00 OK
r-oldrel-osx-x86_64 1.0.3 OK

Check Details

Version: 1.0.2
Check: tests
Result: ERROR
     Running 'testthat.R' [8s/9s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(dbparser)
     >
     > test_check("dbparser")
     -- 1. Error: Read database (@test_drug_all_nodes_parser.R#15) -----------------
     cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/dbparser/extdata/drugbank_record.xml': Read-only file system
     1: expect_true(get_xml_db_rows(system.file("extdata", "drugbank_record.zip", package = "dbparser"))) at testthat/test_drug_all_nodes_parser.R:15
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_xml_db_rows(system.file("extdata", "drugbank_record.zip", package = "dbparser"))
     5: tryCatch({
     db <- unzip(xml_db_name, exdir = dir_name)
     db <- unzip(xml_db_name, list = TRUE)
     xml_db_name <- paste0(dir_name, "/", db$Name[1])
     message(xml_db_name)
     }, error = function(e) {
     stop(e)
     })
     6: tryCatchList(expr, classes, parentenv, handlers)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: value[[3L]](cond)
    
     [1] "Parsed Drugs main attributes, 1/75"
     [1] "Parsed Groups_Drug, 2/75"
     [1] "Parsed Articles_Drug, 3/75"
     [1] "Parsed Books_Drug, 4/75"
     [1] "Parsed Links_Drug, 5/75"
     [1] "Parsed Synonyms_Drug, 6/75"
     [1] "Parsed Products_Drug, 7/75"
     [1] "Parsed Mixtures_Drug, 8/75"
     [1] "Parsed Packagers_Drug, 9/75"
     [1] "Parsed Categories_Drug, 10/75"
     [1] "Parsed Affected_Organisms_Drug, 11/75"
     [1] "Parsed Dosages_Drug, 12/75"
     [1] "Parsed AHFS_Codes_Drug, 13/75"
     [1] "Parsed PDB_Entries_Drug, 14/75"
     [1] "Parsed Patents_Drug, 15/75"
     [1] "Parsed Food_Interactions_Drug, 16/75"
     [1] "Parsed Interactions_Drug, 17/75"
     [1] "Parsed Experimental_Properties_Drug, 18/75"
     [1] "Parsed External_Identifiers_Drug, 19/75"
     [1] "Parsed External_Links_Drug, 20/75"
     [1] "Parsed SNP_Effects_Drug, 21/75"
     [1] "Parsed SNP_Adverse_Drug_Reactions_Drug, 22/75"
     [1] "Parsed ATC_Codes_Drug, 23/75"
     [1] "Parsed Actions_Carrier_Drug, 24/75"
     [1] "Parsed Articles_Carrier_Drug, 25/75"
     [1] "Parsed Textbooks_Carrier_Drug, 26/75"
     [1] "Parsed Links_Carrier_Drug, 27/75"
     [1] "Parsed Polypeptides_Carrier_Drug, 28/75"
     [1] "Parsed External_Identifiers_Polypeptide_Carrier_Drug, 29/75"
     [1] "Parsed Synonyms_Polypeptide_Carrier_Drug, 30/75"
     [1] "Parsed PFAMS_Polypeptide_Carrier_Drug, 31/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Carrier_Drug, 32/75"
     [1] "Parsed Carriers_Drug, 33/75"
     [1] "Parsed Classifications_Drug, 34/75"
     [1] "Parsed Actions_Enzyme_Drug, 35/75"
     [1] "Parsed Articles_Enzyme_Drug, 36/75"
     [1] "Parsed Textbooks_Enzyme_Drug, 37/75"
     [1] "Parsed Links_Enzyme_Drug, 38/75"
     [1] "Parsed Polypeptides_Enzyme_Drug, 39/75"
     [1] "Parsed External_Identifiers_Polypeptides_Enzyme_Drug, 40/75"
     [1] "Parsed Synonyms_Polypeptides_Enzyme_Drug, 41/75"
     [1] "Parsed PFAMS_Polypeptides_Enzyme_Drug, 42/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Enzyme_Drug, 43/75"
     [1] "Parsed Enzyme_Drug, 44/75"
     [1] "Parsed Manufacturers_Drug, 45/75"
     [1] "Parsed Enzymes_Pathway_Drug, 46/75"
     [1] "Parsed drug_pathway_drugs, 47/75"
     [1] "Parsed Pathways_Drug, 48/75"
     [1] "Parsed Prices_Drug, 49/75"
     [1] "Parsed Reactions_Drug, 50/75"
     [1] "Parsed Enzymes_Reactions_Drug, 51/75"
     [1] "Parsed Sequences_Drug, 52/75"
     [1] "Parsed External_Identifiers_Polypeptide_Target_Drug, 53/75"
     [1] "Parsed Synonyms_Polypeptide_Target_Drug, 54/75"
     [1] "Parsed PFAMS_Polypeptide_Target_Drug, 55/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Target_Drug attributes, 56/75"
     [1] "Parsed Actions_Target_Drug, 57/75"
     [1] "Parsed Articles_Target_Drug, 58/75"
     [1] "Parsed Textbooks_Target_Drug, 59/75"
     [1] "Parsed Links_Target_Drug, 60/75"
     [1] "Parsed Polypeptide_Target_Drug, 61/75"
     [1] "Parsed Targets_Drug, 62/75"
     [1] "Parsed Actions_Transporter_Drug, 63/75"
     [1] "Parsed Articles_Transporter_Drug, 64/75"
     [1] "Parsed Textbooks_Transporter_Drug, 65/75"
     [1] "Parsed Links_Transporter_Drug, 66/75"
     [1] "Parsed Polypeptides_Transporter_Drug, 67/75"
     [1] "Parsed External_Identifiers_Transporter_Drug, 68/75"
     [1] "Parsed Synonyms_Polypeptides_Transporter_Drug, 69/75"
     [1] "Parsed PFAMS_Polypeptides_Transporter_Drug, 70/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Transporter_Drug, 71/75"
     [1] "Parsed Transporters_Drug, 72/75"
     [1] "Parsed International_Brands_Drug, 73/75"
     [1] "Parsed Salts_Drug, 74/75"
     [1] "Parsed Calculated_Properties_Drug, 75/75"
     [1] "Parsed Drugs main attributes, 1/75"
     [1] "Parsed Groups_Drug, 2/75"
     [1] "Parsed Articles_Drug, 3/75"
     [1] "Parsed Books_Drug, 4/75"
     [1] "Parsed Links_Drug, 5/75"
     [1] "Parsed Synonyms_Drug, 6/75"
     [1] "Parsed Products_Drug, 7/75"
     [1] "Parsed Mixtures_Drug, 8/75"
     [1] "Parsed Packagers_Drug, 9/75"
     [1] "Parsed Categories_Drug, 10/75"
     [1] "Parsed Affected_Organisms_Drug, 11/75"
     [1] "Parsed Dosages_Drug, 12/75"
     [1] "Parsed AHFS_Codes_Drug, 13/75"
     [1] "Parsed PDB_Entries_Drug, 14/75"
     [1] "Parsed Patents_Drug, 15/75"
     [1] "Parsed Food_Interactions_Drug, 16/75"
     [1] "Parsed Interactions_Drug, 17/75"
     [1] "Parsed Experimental_Properties_Drug, 18/75"
     [1] "Parsed External_Identifiers_Drug, 19/75"
     [1] "Parsed External_Links_Drug, 20/75"
     [1] "Parsed SNP_Effects_Drug, 21/75"
     [1] "Parsed SNP_Adverse_Drug_Reactions_Drug, 22/75"
     [1] "Parsed ATC_Codes_Drug, 23/75"
     [1] "Parsed Actions_Carrier_Drug, 24/75"
     [1] "Parsed Articles_Carrier_Drug, 25/75"
     [1] "Parsed Textbooks_Carrier_Drug, 26/75"
     [1] "Parsed Links_Carrier_Drug, 27/75"
     [1] "Parsed Polypeptides_Carrier_Drug, 28/75"
     [1] "Parsed External_Identifiers_Polypeptide_Carrier_Drug, 29/75"
     [1] "Parsed Synonyms_Polypeptide_Carrier_Drug, 30/75"
     [1] "Parsed PFAMS_Polypeptide_Carrier_Drug, 31/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Carrier_Drug, 32/75"
     [1] "Parsed Carriers_Drug, 33/75"
     [1] "Parsed Classifications_Drug, 34/75"
     [1] "Parsed Actions_Enzyme_Drug, 35/75"
     [1] "Parsed Articles_Enzyme_Drug, 36/75"
     [1] "Parsed Textbooks_Enzyme_Drug, 37/75"
     [1] "Parsed Links_Enzyme_Drug, 38/75"
     [1] "Parsed Polypeptides_Enzyme_Drug, 39/75"
     [1] "Parsed External_Identifiers_Polypeptides_Enzyme_Drug, 40/75"
     [1] "Parsed Synonyms_Polypeptides_Enzyme_Drug, 41/75"
     [1] "Parsed PFAMS_Polypeptides_Enzyme_Drug, 42/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Enzyme_Drug, 43/75"
     [1] "Parsed Enzyme_Drug, 44/75"
     [1] "Parsed Manufacturers_Drug, 45/75"
     [1] "Parsed Enzymes_Pathway_Drug, 46/75"
     [1] "Parsed drug_pathway_drugs, 47/75"
     [1] "Parsed Pathways_Drug, 48/75"
     [1] "Parsed Prices_Drug, 49/75"
     [1] "Parsed Reactions_Drug, 50/75"
     [1] "Parsed Enzymes_Reactions_Drug, 51/75"
     [1] "Parsed Sequences_Drug, 52/75"
     [1] "Parsed External_Identifiers_Polypeptide_Target_Drug, 53/75"
     [1] "Parsed Synonyms_Polypeptide_Target_Drug, 54/75"
     [1] "Parsed PFAMS_Polypeptide_Target_Drug, 55/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Target_Drug attributes, 56/75"
     [1] "Parsed Actions_Target_Drug, 57/75"
     [1] "Parsed Articles_Target_Drug, 58/75"
     [1] "Parsed Textbooks_Target_Drug, 59/75"
     [1] "Parsed Links_Target_Drug, 60/75"
     [1] "Parsed Polypeptide_Target_Drug, 61/75"
     [1] "Parsed Targets_Drug, 62/75"
     [1] "Parsed Actions_Transporter_Drug, 63/75"
     [1] "Parsed Articles_Transporter_Drug, 64/75"
     [1] "Parsed Textbooks_Transporter_Drug, 65/75"
     [1] "Parsed Links_Transporter_Drug, 66/75"
     [1] "Parsed Polypeptides_Transporter_Drug, 67/75"
     [1] "Parsed External_Identifiers_Transporter_Drug, 68/75"
     [1] "Parsed Synonyms_Polypeptides_Transporter_Drug, 69/75"
     [1] "Parsed PFAMS_Polypeptides_Transporter_Drug, 70/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Transporter_Drug, 71/75"
     [1] "Parsed Transporters_Drug, 72/75"
     [1] "Parsed International_Brands_Drug, 73/75"
     [1] "Parsed Salts_Drug, 74/75"
     [1] "Parsed Calculated_Properties_Drug, 75/75"
     [1] "Parsed Drugs main attributes, 1/75"
     [1] "Parsed Groups_Drug, 2/75"
     [1] "Parsed Articles_Drug, 3/75"
     [1] "Parsed Books_Drug, 4/75"
     [1] "Parsed Links_Drug, 5/75"
     [1] "Parsed Synonyms_Drug, 6/75"
     [1] "Parsed Products_Drug, 7/75"
     [1] "Parsed Mixtures_Drug, 8/75"
     [1] "Parsed Packagers_Drug, 9/75"
     [1] "Parsed Categories_Drug, 10/75"
     [1] "Parsed Affected_Organisms_Drug, 11/75"
     [1] "Parsed Dosages_Drug, 12/75"
     [1] "Parsed AHFS_Codes_Drug, 13/75"
     [1] "Parsed PDB_Entries_Drug, 14/75"
     [1] "Parsed Patents_Drug, 15/75"
     [1] "Parsed Food_Interactions_Drug, 16/75"
     [1] "Parsed Interactions_Drug, 17/75"
     [1] "Parsed Experimental_Properties_Drug, 18/75"
     [1] "Parsed External_Identifiers_Drug, 19/75"
     [1] "Parsed External_Links_Drug, 20/75"
     [1] "Parsed SNP_Effects_Drug, 21/75"
     [1] "Parsed SNP_Adverse_Drug_Reactions_Drug, 22/75"
     [1] "Parsed ATC_Codes_Drug, 23/75"
     [1] "Parsed Actions_Carrier_Drug, 24/75"
     [1] "Parsed Articles_Carrier_Drug, 25/75"
     [1] "Parsed Textbooks_Carrier_Drug, 26/75"
     [1] "Parsed Links_Carrier_Drug, 27/75"
     [1] "Parsed Polypeptides_Carrier_Drug, 28/75"
     [1] "Parsed External_Identifiers_Polypeptide_Carrier_Drug, 29/75"
     [1] "Parsed Synonyms_Polypeptide_Carrier_Drug, 30/75"
     [1] "Parsed PFAMS_Polypeptide_Carrier_Drug, 31/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Carrier_Drug, 32/75"
     [1] "Parsed Carriers_Drug, 33/75"
     [1] "Parsed Classifications_Drug, 34/75"
     [1] "Parsed Actions_Enzyme_Drug, 35/75"
     [1] "Parsed Articles_Enzyme_Drug, 36/75"
     [1] "Parsed Textbooks_Enzyme_Drug, 37/75"
     [1] "Parsed Links_Enzyme_Drug, 38/75"
     [1] "Parsed Polypeptides_Enzyme_Drug, 39/75"
     [1] "Parsed External_Identifiers_Polypeptides_Enzyme_Drug, 40/75"
     [1] "Parsed Synonyms_Polypeptides_Enzyme_Drug, 41/75"
     [1] "Parsed PFAMS_Polypeptides_Enzyme_Drug, 42/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Enzyme_Drug, 43/75"
     [1] "Parsed Enzyme_Drug, 44/75"
     [1] "Parsed Manufacturers_Drug, 45/75"
     [1] "Parsed Enzymes_Pathway_Drug, 46/75"
     [1] "Parsed drug_pathway_drugs, 47/75"
     [1] "Parsed Pathways_Drug, 48/75"
     [1] "Parsed Prices_Drug, 49/75"
     [1] "Parsed Reactions_Drug, 50/75"
     [1] "Parsed Enzymes_Reactions_Drug, 51/75"
     [1] "Parsed Sequences_Drug, 52/75"
     [1] "Parsed External_Identifiers_Polypeptide_Target_Drug, 53/75"
     [1] "Parsed Synonyms_Polypeptide_Target_Drug, 54/75"
     [1] "Parsed PFAMS_Polypeptide_Target_Drug, 55/75"
     [1] "Parsed GO_Classifiers_Polypeptide_Target_Drug attributes, 56/75"
     [1] "Parsed Actions_Target_Drug, 57/75"
     [1] "Parsed Articles_Target_Drug, 58/75"
     [1] "Parsed Textbooks_Target_Drug, 59/75"
     [1] "Parsed Links_Target_Drug, 60/75"
     [1] "Parsed Polypeptide_Target_Drug, 61/75"
     [1] "Parsed Targets_Drug, 62/75"
     [1] "Parsed Actions_Transporter_Drug, 63/75"
     [1] "Parsed Articles_Transporter_Drug, 64/75"
     [1] "Parsed Textbooks_Transporter_Drug, 65/75"
     [1] "Parsed Links_Transporter_Drug, 66/75"
     [1] "Parsed Polypeptides_Transporter_Drug, 67/75"
     [1] "Parsed External_Identifiers_Transporter_Drug, 68/75"
     [1] "Parsed Synonyms_Polypeptides_Transporter_Drug, 69/75"
     [1] "Parsed PFAMS_Polypeptides_Transporter_Drug, 70/75"
     [1] "Parsed GO_Classifiers_Polypeptides_Transporter_Drug, 71/75"
     [1] "Parsed Transporters_Drug, 72/75"
     [1] "Parsed International_Brands_Drug, 73/75"
     [1] "Parsed Salts_Drug, 74/75"
     [1] "Parsed Calculated_Properties_Drug, 75/75"
     [1] "Parsed AHFS_Codes_Drug"
     [1] "Parsed Affected_Organisms_Drug"
     [1] "Parsed Textbooks_Transporter_Drug"
     == testthat results ===========================================================
     OK: 325 SKIPPED: 0 WARNINGS: 0 FAILED: 1
     1. Error: Read database (@test_drug_all_nodes_parser.R#15)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang