* using log directory 'd:/Rcompile/CRANpkg/local/4.1/cbioportalR.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'cbioportalR/DESCRIPTION' ... OK * this is package 'cbioportalR' version '1.0.0' * package encoding: UTF-8 * 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 whether package 'cbioportalR' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 R 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 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 ... [7s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [28s] ERROR Running examples in 'cbioportalR-Ex.R' failed The error most likely occurred in: > ### Name: get_fusions_by_study > ### Title: Get Fusions By Study > ### Aliases: get_fusions_by_study > > ### ** Examples > > ## Don't show: > if (!httr::http_error("www.cbioportal.org/api")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf + ## End(Don't show) + get_fusions_by_study(molecular_profile_id = "prad_msk_2019_fusion") + ## Don't show: + }) # examplesIf > get_fusions_by_study(molecular_profile_id = "prad_msk_2019_fusion") Error in `.lookup_study_name()`: ! Molecular profile "prad_msk_2019_fusion" doesn't exist, or molecular profile doesn't match the "study_id" you passed. See `available_profiles()` or `available_studies()` Backtrace: x 1. +-(if (getRversion() >= "3.4") withAutoprint else force)(...) 2. | \-base::source(...) 3. | +-base::withVisible(eval(ei, envir)) 4. | \-base::eval(ei, envir) 5. | \-base::eval(ei, envir) 6. \-cbioportalR::get_fusions_by_study(molecular_profile_id = "prad_msk_2019_fusion") 7. \-cbioportalR::.get_data_by_study(...) 8. \-cbioportalR::.lookup_study_name(molecular_profile_id = molecular_profile_id, study_id = study_id, base_url = base_url) 9. \-cli::cli_abort("Molecular profile {.val {molecular_profile_id}} doesn't exist, or molecular profile doesn't match the {.val study_id} you passed. See {.code available_profiles()} or {.code available_studies()}") 10. \-rlang::abort(message, ..., call = call, use_cli_format = TRUE) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [378s] ERROR Running 'spelling.R' [0s] Running 'testthat.R' [378s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(cbioportalR) > > test_check("cbioportalR") v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i No `study_id` provided. Returning all available genomic profiles for v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i No `study_id` provided. Using "msk_impact_2017" as default study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i No `study_id` provided. Using "msk_impact_2017" as default study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "blca_nmibc_2017" study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_cna" Genes: "All available genes" ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "prad_msk_2019" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "msk_impact_2017" Molecular Profile ID: "msk_impact_2017_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "msk_impact_2017" Molecular Profile ID: "msk_impact_2017_cna" Genes: "All available genes" ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_nmibc_2017" and "msk_impact_2017" Molecular Profile ID: blca_nmibc_2017_mutations and msk_impact_2017_mutations Genes: "All available genes" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_nmibc_2017" and "msk_impact_2017" Molecular Profile ID: blca_nmibc_2017_cna and msk_impact_2017_cna Genes: "All available genes" ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "blca_nmibc_2017" study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_nmibc_2017" and "msk_impact_2017" Molecular Profile ID: blca_nmibc_2017_mutations and msk_impact_2017_mutations Genes: "All available genes" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_nmibc_2017" and "msk_impact_2017" Molecular Profile ID: blca_nmibc_2017_cna and msk_impact_2017_cna Genes: "All available genes" ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "blca_nmibc_2017" study ! No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "msk_impact_2017" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" ! Sample Level Clinical Data: No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "mpnst_mskcc" study ! Patient Level Clinical Data: No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_structural_variants" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_structural_variants" molecular profile in the "mpnst_mskcc" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i No `study_id` provided. Returning all available genomic profiles for v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" ! Patient Level Clinical Data: No `clinical_attribute` passed. Defaulting to returning all clinical attributes in "acc_tcga" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" List of 2 $ :List of 3 ..$ entrezGeneId : int 7157 ..$ hugoGeneSymbol: chr "TP53" ..$ type : chr "protein-coding" $ :List of 3 ..$ entrezGeneId : int 2260 ..$ hugoGeneSymbol: chr "FGFR1" ..$ type : chr "protein-coding" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_mutations" Genes: "All available genes" ! You have passed both a `study_id` AND `molecular_profile_id`. Ignoring `study_id` ! You have passed both a `study_id` AND `molecular_profile_id`. Ignoring `study_id` The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "msk_impact_2017" Molecular Profile ID: "msk_impact_2017_mutations" Genes: "All available genes" ! You have passed both a `study_id` AND `molecular_profile_id`. Ignoring `study_id` ! You have passed both a `study_id` AND `molecular_profile_id`. Ignoring `study_id` The following parameters were used in query: Study ID: "mpnst_mskcc" Molecular Profile ID: "mpnst_mskcc_mutations" Genes: "All available genes" ! You have passed both a `study_id` AND `molecular_profile_id`. Ignoring `study_id` v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations and prad_msk_2019_mutations Genes: "All available genes" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_mutations" and "prad_msk_2019_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_mutations" and "prad_msk_2019_mutations" Genes: "All available genes" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_cna" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_structural_variants" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_cna" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_cna" Genes: "All available genes" The following parameters were used in query: Study ID: "prad_msk_2019" Molecular Profile ID: "prad_msk_2019_structural_variants" Genes: "All available genes" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_gistic" Genes: "All available genes" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_mutations" Genes: "All available genes" The following parameters were used in query: Study ID: "acc_tcga" Molecular Profile ID: "acc_tcga_gistic" Genes: "All available genes" ! No "fusion" data returned. Error: No molecular profile for `` data_type = `fusion` `` found in "acc_tcga". See `` available_profiles('`acc_tcga`') `` v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_cna" Genes: "All available genes" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_cna" Genes: "All available genes" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_cna" Genes: 25, 84142, 207, 208, 10000, 238, 242, 139285, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 8314, 580, 27113, 596, 598, 10018, 604, 54880, 641, 657, 673, 672, 675, 23476, 83990, 695, 84433, 841, 865, 867, 595, 894, 896, 898, 29126, 80381, 974, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, -2, -1, 1030, 1031, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 1436, 10664, 1493, 1499, 8452, 1616, 54165, 4921, 23405, 22894, 1786, 1788, 1789, 84444, 1871, 8726, 51162, 1956, 1964, 2033, 4072, 2042, 2044, 2047, 2064, 2065, 2066, ... v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "blca_plasmacytoid_mskcc_2016_mutations" molecular profile in the "blca_plasmacytoid_mskcc_2016" study i Returning all data for the "blca_plasmacytoid_mskcc_2016_cna" molecular profile in the "blca_plasmacytoid_mskcc_2016" study i Returning all data for the "blca_plasmacytoid_mskcc_2016_structural_variants" molecular profile in the "blca_plasmacytoid_mskcc_2016" study Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: 2064, 1026, 1969, 4853, 2047, 79633, 5728, 999, 5288, 5295, 10111, 6098, 5288, 2033, 5156, 1026, 5288, 8929, 7015, 545, 7157, 8085, 8085, 999, 54894, 4297, 2065, 1009, 999, 55193, 2051, 5789, 999, 8085, 4854, 5594, 2033, 999, 8289, 5295, 5925, 7157, 79633, 4855, 999, 7015, 5290, 5290, 5290, 5789, 999, 171023, 6790, 4771, 1026, 2047, 2073, 1026, 7157, 58508, 999, 2737, 999, 7157, 11122, 5925, 5290, 11122, 4297, 4613, 23451, 3667, 55294, 5295, 5159, 10413, 5426, 1024, 999, 9817, 2068, 8289, 545, 6657, 5295, 4233, 2065, 1024, 675, 7525, 2042, 5925, 7157, 2475, 4297, 999, 142, 6198, 1026, 6608, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: 2064, 1026, 1969, 4853, 2047, 79633, 5728, 999, 5288, 5295, 10111, 6098, 5288, 2033, 5156, 1026, 5288, 8929, 7015, 545, 7157, 8085, 8085, 999, 54894, 4297, 2065, 1009, 999, 55193, 2051, 5789, 999, 8085, 4854, 5594, 2033, 999, 8289, 5295, 5925, 7157, 79633, 4855, 999, 7015, 5290, 5290, 5290, 5789, 999, 171023, 6790, 4771, 1026, 2047, 2073, 1026, 7157, 58508, 999, 2737, 999, 7157, 11122, 5925, 5290, 11122, 4297, 4613, 23451, 3667, 55294, 5295, 5159, 10413, 5426, 1024, 999, 9817, 2068, 8289, 545, 6657, 5295, 4233, 2065, 1024, 675, 7525, 2042, 5925, 7157, 2475, 4297, 999, 142, 6198, 1026, 6608, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: 2064, 1026, 1969, 4853, 2047, 79633, 5728, 999, 5288, 5295, 10111, 6098, 5288, 2033, 5156, 1026, 5288, 8929, 7015, 545, 7157, 8085, 8085, 999, 54894, 4297, 2065, 1009, 999, 55193, 2051, 5789, 999, 8085, 4854, 5594, 2033, 999, 8289, 5295, 5925, 7157, 79633, 4855, 999, 7015, 5290, 5290, 5290, 5789, 999, 171023, 6790, 4771, 1026, 2047, 2073, 1026, 7157, 58508, 999, 2737, 999, 7157, 11122, 5925, 5290, 11122, 4297, 4613, 23451, 3667, 55294, 5295, 5159, 10413, 5426, 1024, 999, 9817, 2068, 8289, 545, 6657, 5295, 4233, 2065, 1024, 675, 7525, 2042, 5925, 7157, 2475, 4297, 999, 142, 6198, 1026, 6608, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "RB1", "EPHB6", "SMARCB1", "IRS1", "MPL", "ARAF", "KEAP1", "BUB1B", "IRS2", "IGF1R", "RPS6KA4", "SOX2", "STK11", "CDH1", "CHEK2", "PIM1", "KDR", "EP300", "AKT1", "NBN", "ARID2", "ROS1", "EPHB1", "PDGFRB", "EPHA5", "RNF43", "MAP2K4", "PDGFRA", "FBXW7", "MAGI2", "TSC2", "TSC1", "DICER1", "HNF1A", "RUNX1", "INPP4A", "MSH6", "AR", "MYCN", "SMO", "TP53", "EPHA3", "EPHA2", "NOTCH2", "KMT2D", "NOTCH3", "CSF1R", "DNMT1", "BLM", "NOTCH1", "KMT2A", "KMT2C", "CUL3", "NOTCH4", "PIK3R3", "PIK3R1", "HIF1A", "COP1", "GRIN2A", "TERT", "ABL2", "MCL1", "SMAD2", "CREBBP", "YES1", "SMAD3", "PTCH1", "BRAF", "PALB2", "PHOX2B", "SMARCA4", "H1-2", "PTPRD", "CDK8", "STAG2", "REL", "NF1", "GNAS", "FAT1", "ATM", "FAT4", "CDK12", "NF2", "IL7R", "FGFR3", "BAP1", "MYD88", "FGFR2", "EZH2", "ATR", "PTPRT", "KDM5A", "ALK", "SETD2", "CDKN1A", "PTPRS", "FLT4", "PTEN", "PIK3CD", "PIK3C2G", ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "RB1", "EPHB6", "SMARCB1", "IRS1", "MPL", "ARAF", "KEAP1", "BUB1B", "IRS2", "IGF1R", "RPS6KA4", "SOX2", "STK11", "CDH1", "CHEK2", "PIM1", "KDR", "EP300", "AKT1", "NBN", "ARID2", "ROS1", "EPHB1", "PDGFRB", "EPHA5", "RNF43", "MAP2K4", "PDGFRA", "FBXW7", "MAGI2", "TSC2", "TSC1", "DICER1", "HNF1A", "RUNX1", "INPP4A", "MSH6", "AR", "MYCN", "SMO", "TP53", "EPHA3", "EPHA2", "NOTCH2", "KMT2D", "NOTCH3", "CSF1R", "DNMT1", "BLM", "NOTCH1", "KMT2A", "KMT2C", "CUL3", "NOTCH4", "PIK3R3", "PIK3R1", "HIF1A", "COP1", "GRIN2A", "TERT", "ABL2", "MCL1", "SMAD2", "CREBBP", "YES1", "SMAD3", "PTCH1", "BRAF", "PALB2", "PHOX2B", "SMARCA4", "H1-2", "PTPRD", "CDK8", "STAG2", "REL", "NF1", "GNAS", "FAT1", "ATM", "FAT4", "CDK12", "NF2", "IL7R", "FGFR3", "BAP1", "MYD88", "FGFR2", "EZH2", "ATR", "PTPRT", "KDM5A", "ALK", "SETD2", "CDKN1A", "PTPRS", "FLT4", "PTEN", "PIK3CD", "PIK3C2G", ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "RB1", "EPHB6", "SMARCB1", "IRS1", "MPL", "ARAF", "KEAP1", "BUB1B", "IRS2", "IGF1R", "RPS6KA4", "SOX2", "STK11", "CDH1", "CHEK2", "PIM1", "KDR", "EP300", "AKT1", "NBN", "ARID2", "ROS1", "EPHB1", "PDGFRB", "EPHA5", "RNF43", "MAP2K4", "PDGFRA", "FBXW7", "MAGI2", "TSC2", "TSC1", "DICER1", "HNF1A", "RUNX1", "INPP4A", "MSH6", "AR", "MYCN", "SMO", "TP53", "EPHA3", "EPHA2", "NOTCH2", "KMT2D", "NOTCH3", "CSF1R", "DNMT1", "BLM", "NOTCH1", "KMT2A", "KMT2C", "CUL3", "NOTCH4", "PIK3R3", "PIK3R1", "HIF1A", "COP1", "GRIN2A", "TERT", "ABL2", "MCL1", "SMAD2", "CREBBP", "YES1", "SMAD3", "PTCH1", "BRAF", "PALB2", "PHOX2B", "SMARCA4", "H1-2", "PTPRD", "CDK8", "STAG2", "REL", "NF1", "GNAS", "FAT1", "ATM", "FAT4", "CDK12", "NF2", "IL7R", "FGFR3", "BAP1", "MYD88", "FGFR2", "EZH2", "ATR", "PTPRT", "KDM5A", "ALK", "SETD2", "CDKN1A", "PTPRS", "FLT4", "PTEN", "PIK3CD", "PIK3C2G", ... v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: 4853, 1026, 2064, 5288, and 1969 Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: 4853, 1026, 2064, 5288, and 1969 Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: 4853, 1026, 2064, 5288, and 1969 Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "NOTCH2", "CDKN1A", "ERBB2", "PIK3C2G", and "EPHA2" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "NOTCH2", "CDKN1A", "ERBB2", "PIK3C2G", and "EPHA2" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "NOTCH2", "CDKN1A", "ERBB2", "PIK3C2G", and "EPHA2" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "IMPACT468" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: 25, 84142, 90, 27161, 207, 208, 10000, 238, 242, 139285, 29123, 324, 367, 369, 8289, 57492, 196528, 84159, 171023, 55252, 472, 545, 546, 6790, 9212, 8312, 8313, 558, 567, 29086, 8314, 580, 27113, 8915, 596, 598, 10018, 604, 54880, 330, 641, 657, 673, 672, 675, 23476, 83990, 695, 811, 84433, 10498, 841, 865, 867, 595, 894, 896, 898, 92002, 29126, 80381, 973, 974, 998, 79577, 999, 51755, 1019, 1021, 1024, 1026, 1027, 1029, 1030, 1031, 1050, 1058, 1111, 11200, 23152, 64326, 1387, 1399, 64109, 7812, 1436, 1441, 10664, 1493, 1499, 8452, 7852, 1540, 57105, 1616, 54165, 4921, 23405, 22894, 3337, ... v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "sarc_mskcc_panel" and "NOTCH4" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "sarc_mskcc_panel" and "NOTCH4" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "sarc_mskcc_panel" and "NOTCH4" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "sarc_mskcc_panel" and "4855" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "sarc_mskcc_panel" and "4855" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "sarc_mskcc_panel" and "4855" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations Genes: "sarc_mskcc_panel" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna Genes: "sarc_mskcc_panel" Joining, by = "study_id" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants Genes: "sarc_mskcc_panel" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_mutations" Genes: "IMPACT468", "sarc_mskcc_panel", and "NOTCH2" The following parameters were used in query: Study ID: "blca_plasmacytoid_mskcc_2016" Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_mutations" Genes: "sarc_mskcc_panel" and "NOTCH2" v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_structural_variants" molecular profile in the "mpnst_mskcc" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "acc_tcga_mutations" molecular profile in the "acc_tcga" study i Returning all data for the "acc_tcga_mutations" molecular profile in the "acc_tcga" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_structural_variants" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_mutations" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_cna" molecular profile in the "mpnst_mskcc" study i Returning all data for the "mpnst_mskcc_structural_variants" molecular profile in the "mpnst_mskcc" study v You are successfully connected! v base_url for this R session is now set to "www.cbioportal.org/api" i Returning all data for the "acc_tcga_gistic" molecular profile in the "acc_tcga" study ! No "fusion" data returned. Error: No molecular profile for `` data_type = `fusion` `` found in "acc_tcga". See `` available_profiles('`acc_tcga`') `` [ FAIL 2 | WARN 0 | SKIP 0 | PASS 152 ] == Failed tests ================================================================ -- Error (test-genomics-by-sample.R:225:3): data is same regardless of function -- Error in `.lookup_study_name(molecular_profile_id = molecular_profile_id, study_id = ., base_url = base_url)`: Molecular profile "prad_msk_2019_fusion" doesn't exist, or molecular profile doesn't match the "study_id" you passed. See `available_profiles()` or `available_studies()` Backtrace: x 1. +-cbioportalR::get_fusions_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id) at test-genomics-by-sample.R:225:2 2. | \-cbioportalR::.get_data_by_sample(...) 3. | \-study_id %>% ... 4. \-purrr::when(...) 5. \-base::eval(dots[[i]][[action]], env, env) 6. \-base::eval(dots[[i]][[action]], env, env) 7. \-cbioportalR::.lookup_study_name(molecular_profile_id = molecular_profile_id, study_id = ., base_url = base_url) 8. \-cli::cli_abort("Molecular profile {.val {molecular_profile_id}} doesn't exist, or molecular profile doesn't match the {.val study_id} you passed. See {.code available_profiles()} or {.code available_studies()}") 9. \-rlang::abort(message, ..., call = call, use_cli_format = TRUE) -- Error (test-genomics-by-study.R:173:3): data is same regardless of function -- Error in `.lookup_study_name(molecular_profile_id = molecular_profile_id, study_id = study_id, base_url = base_url)`: Molecular profile "mpnst_mskcc_fusion" doesn't exist, or molecular profile doesn't match the "study_id" you passed. See `available_profiles()` or `available_studies()` Backtrace: x 1. \-cbioportalR::get_fusions_by_study(molecular_profile_id = molecular_profile_id) at test-genomics-by-study.R:173:2 2. \-cbioportalR::.get_data_by_study(...) 3. \-cbioportalR::.lookup_study_name(molecular_profile_id = molecular_profile_id, study_id = study_id, base_url = base_url) 4. \-cli::cli_abort("Molecular profile {.val {molecular_profile_id}} doesn't exist, or molecular profile doesn't match the {.val study_id} you passed. See {.code available_profiles()} or {.code available_studies()}") 5. \-rlang::abort(message, ..., call = call, use_cli_format = TRUE) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 152 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [4s] OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs