Running ‘runTests.R’ [1s/3s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > library(testthat)
  > library(cgdsr)
  Please send questions to cbioportal@googlegroups.com
  > test_package("cgdsr")
  ── 1. Error: getCancerStudies (@test_cgdsr.R#6)  ───────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getCancerStudies&'
  1: getCancerStudies(mycgds) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:6
  2: getCancerStudies.CGDS(mycgds)
  3: processURL(x, url)
  4: processURL.CGDS(x, url)
  5: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  6: file(file, "rt")
  
  ── 2. Error: getCaseLists (@test_cgdsr.R#12)  ──────────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getCancerStudies&'
  1: getCancerStudies(mycgds) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:12
  2: getCancerStudies.CGDS(mycgds)
  3: processURL(x, url)
  4: processURL.CGDS(x, url)
  5: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  6: file(file, "rt")
  
  ── 3. Error: getGeneticProfiles (@test_cgdsr.R#23)  ────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getCancerStudies&'
  1: getCancerStudies(mycgds) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:23
  2: getCancerStudies.CGDS(mycgds)
  3: processURL(x, url)
  4: processURL.CGDS(x, url)
  5: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  6: file(file, "rt")
  
  ── 4. Error: getMutationData (@test_cgdsr.R#38)  ───────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getMutationData&case_set_id=lusc_tcga_pub_sequenced&genetic_profile_id=lusc_tcga_pub_mutations&gene_list=AURKB'
  1: expect_equal(nrow(getMutationData(mycgds, "lusc_tcga_pub_sequenced", "lusc_tcga_pub_mutations", 
         "AURKB")), 0) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:38
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: nrow(getMutationData(mycgds, "lusc_tcga_pub_sequenced", "lusc_tcga_pub_mutations", 
         "AURKB"))
  5: getMutationData(mycgds, "lusc_tcga_pub_sequenced", "lusc_tcga_pub_mutations", "AURKB")
  6: getMutationData.CGDS(mycgds, "lusc_tcga_pub_sequenced", "lusc_tcga_pub_mutations", 
         "AURKB")
  7: processURL(x, url)
  8: processURL.CGDS(x, url)
  9: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  10: file(file, "rt")
  
  ── 5. Error: getClinicalData (@test_cgdsr.R#44)  ───────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getClinicalData&case_set_id=gbm_tcga_all'
  1: expect_true("DFS_MONTHS" %in% colnames(getClinicalData(mycgds, "gbm_tcga_all"))) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:44
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: "DFS_MONTHS" %in% colnames(getClinicalData(mycgds, "gbm_tcga_all"))
  5: colnames(getClinicalData(mycgds, "gbm_tcga_all"))
  6: is.data.frame(x)
  7: getClinicalData(mycgds, "gbm_tcga_all")
  8: getClinicalData.CGDS(mycgds, "gbm_tcga_all")
  9: processURL(x, url)
  10: processURL.CGDS(x, url)
  11: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  12: file(file, "rt")
  
  ── 6. Error: getProfileData (@test_cgdsr.R#51)  ────────────────────────────────
  cannot open the connection to 'http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=NF1&genetic_profile_id=gbm_tcga_mrna&id_type=gene_symbol&case_set_id=gbm_tcga_all'
  1: expect_identical(colnames(getProfileData(mycgds, "NF1", "gbm_tcga_mrna", "gbm_tcga_all")), 
         "NF1") at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cgdsr/tests/test_cgdsr.R:51
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: colnames(getProfileData(mycgds, "NF1", "gbm_tcga_mrna", "gbm_tcga_all"))
  5: is.data.frame(x)
  6: getProfileData(mycgds, "NF1", "gbm_tcga_mrna", "gbm_tcga_all")
  7: getProfileData.CGDS(mycgds, "NF1", "gbm_tcga_mrna", "gbm_tcga_all")
  8: processURL(x, url)
  9: processURL.CGDS(x, url)
  10: read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t", quote = "")
  11: file(file, "rt")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 6
  1. Error: getCancerStudies (@test_cgdsr.R#6) 
  2. Error: getCaseLists (@test_cgdsr.R#12) 
  3. Error: getGeneticProfiles (@test_cgdsr.R#23) 
  4. Error: getMutationData (@test_cgdsr.R#38) 
  5. Error: getClinicalData (@test_cgdsr.R#44) 
  6. Error: getProfileData (@test_cgdsr.R#51) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted