* using log directory 'd:/RCompile/CRANincoming/R-devel/SPARQLchunks.Rcheck' * using R Under development (unstable) (2025-06-27 r88363 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'SPARQLchunks/DESCRIPTION' ... OK * this is package 'SPARQLchunks' version '0.4' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Andre Ourednik ' New submission * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'SPARQLchunks' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... NOTE Found the following assignments to the global environment: File 'SPARQLchunks/R/sparqlchunks.R': assign(varname, out, envir = knitr::knit_global()) * checking Rd files ... 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 ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Complete output: > # 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [12s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs