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Type 'q()' to quit R. > # 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SPARQLchunks) Run `knitr::knit_engines$set(sparql = SPARQLchunks::eng_sparql)` in your Rmd setup chunk to be able to execute SPARQL chunks. > > test_check("SPARQLchunks") Trying to determine proxy parameters No proxy found, nor needed, to access the endpoint https://lindas.admin.ch/query Preparing to send query to: https://sparql.uniprot.org/sparql SPARQL string: PREFIX up: SELECT ?taxon FROM WHERE { ?taxon a up:Taxon . } LIMIT 500 Query URL: https://sparql.uniprot.org/sparql?query=PREFIX%20up%3A%20%3Chttp%3A%2F%2Fpurl.uniprot.org%2Fcore%2F%3E%0ASELECT%20%3Ftaxon%0AFROM%20%3Chttp%3A%2F%2Fsparql.uniprot.org%2Ftaxonomy%3E%0AWHERE%20%7B%0A%09%3Ftaxon%20a%20up%3ATaxon%20.%0A%7D%20LIMIT%20500 The SPARQL query returned 500 results Preparing to send query to: https://sparql.uniprot.org/sparql SPARQL string: PREFIX up: SELECT ?taxon FROM WHERE { ?taxon a up:Taxon . } LIMIT 500 Query URL: https://sparql.uniprot.org/sparql?query=PREFIX%20up%3A%20%3Chttp%3A%2F%2Fpurl.uniprot.org%2Fcore%2F%3E%0ASELECT%20%3Ftaxon%0AFROM%20%3Chttp%3A%2F%2Fsparql.uniprot.org%2Ftaxonomy%3E%0AWHERE%20%7B%0A%09%3Ftaxon%20a%20up%3ATaxon%20.%0A%7D%20LIMIT%20500 The SPARQL query returned 500 results Preparing to send query to: https://sparql.uniprot.org/sparql SPARQL string: PREFIX up: SELECT ?taxon FROM WHERE { ?taxon a up:Taxon . } LIMIT 500 Query URL: https://sparql.uniprot.org/sparql?query=PREFIX%20up%3A%20%3Chttp%3A%2F%2Fpurl.uniprot.org%2Fcore%2F%3E%0ASELECT%20%3Ftaxon%0AFROM%20%3Chttp%3A%2F%2Fsparql.uniprot.org%2Ftaxonomy%3E%0AWHERE%20%7B%0A%09%3Ftaxon%20a%20up%3ATaxon%20.%0A%7D%20LIMIT%20500 The SPARQL query returned 500 results Preparing to send query to: http://example.org/sparql SPARQL string: SELECT * WHERE {?s ?p ?o} Query URL: http://example.org/sparql?query=SELECT%20%2A%20WHERE%20%7B%3Fs%20%3Fp%20%3Fo%7D Preparing to send query to: http://example.org/sparql SPARQL string: SELECT * WHERE {?s ?p ?o} Query URL: http://example.org/sparql?query=SELECT%20%2A%20WHERE%20%7B%3Fs%20%3Fp%20%3Fo%7D trying URL 'http://example.org/sparql?query=SELECT%20%2A%20WHERE%20%7B%3Fs%20%3Fp%20%3Fo%7D' Preparing to send query to: https://lindas.admin.ch/query SPARQL string: PREFIX schema: SELECT * WHERE { ?sub a schema:DataCatalog . ?subtype a schema:DataType . } Query URL: https://lindas.admin.ch/query?query=PREFIX%20schema%3A%20%3Chttp%3A%2F%2Fschema.org%2F%3E%0A%09%20%20%20SELECT%20%2A%20WHERE%20%7B%0A%09%20%20%20%3Fsub%20a%20schema%3ADataCatalog%20.%0A%09%20%20%20%3Fsubtype%20a%20schema%3ADataType%20.%0A%09%7D Trying to determine proxy parameters No proxy found, nor needed, to access the endpoint https://lindas.admin.ch/query Preparing to send query to: https://lindas.admin.ch/query SPARQL string: PREFIX schema: SELECT * WHERE { ?sub a schema:DataCatalog . ?subtype a schema:DataType . } Query URL: https://lindas.admin.ch/query?query=PREFIX%20schema%3A%20%3Chttp%3A%2F%2Fschema.org%2F%3E%0A%09%20%20%20SELECT%20%2A%20WHERE%20%7B%0A%09%20%20%20%3Fsub%20a%20schema%3ADataCatalog%20.%0A%09%20%20%20%3Fsubtype%20a%20schema%3ADataType%20.%0A%09%7D Preparing to send query to: https://sparql.uniprot.org/sparql SPARQL string: PREFIX up: SELECT ?taxon FROM WHERE { ?taxon a up:Taxon . } LIMIT 500 Query URL: https://sparql.uniprot.org/sparql?query=PREFIX%20up%3A%20%3Chttp%3A%2F%2Fpurl.uniprot.org%2Fcore%2F%3E%0ASELECT%20%3Ftaxon%0AFROM%20%3Chttp%3A%2F%2Fsparql.uniprot.org%2Ftaxonomy%3E%0AWHERE%20%7B%0A%09%3Ftaxon%20a%20up%3ATaxon%20.%0A%7D%20LIMIT%20500 [ FAIL 1 | WARN 3 | SKIP 1 | PASS 10 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-get_outcontent.R:77:2' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-get_outcontent.R:121:2'): fallback block is triggered when content is NULL ── Error in `utils::download.file(qm, method = "wininet", headers = c(Accept = acceptype), tempfile)`: cannot open URL 'http://example.org/sparql?query=SELECT%20%2A%20WHERE%20%7B%3Fs%20%3Fp%20%3Fo%7D' Backtrace: ▆ 1. └─SPARQLchunks:::get_outcontent(...) at test-get_outcontent.R:121:9 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) 6. └─utils::download.file(...) [ FAIL 1 | WARN 3 | SKIP 1 | PASS 10 ] Error: Test failures Execution halted