* 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 <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. 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 <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"
! 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"
<GitHub api/genes/fetch>
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