Error in .checkFixSampleMap(sampleMap) #81
Description
Hi! I'm getting the below error for my query:
> cbio_api <- cBioPortal()
> study <- "aml_ohsu_2018"
> samples <- c("aml_ohsu_2018_16-00374", "aml_ohsu_2018_16-00783")
> cBioPortalData(
+ api = cbio_api,
+ by = "hugoGeneSymbol",
+ studyId = study,
+ sampleIds = samples,
+ genePanelId = "Agilent"
+ )
Error in .checkFixSampleMap(sampleMap) :
'sampleMap' does not have required columns
What are the required columns?
Here is the session info:
R Under development (unstable) (2025-01-20 r87609)
Platform: aarch64-unknown-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] cBioPortalData_2.19.9 MultiAssayExperiment_1.33.4 AnVIL_1.19.8 AnVILBase_1.1.0
[5] curatedMetagenomicData_3.15.0 TreeSummarizedExperiment_2.15.0 Biostrings_2.75.3 XVector_0.47.2
[9] SingleCellExperiment_1.29.1 SummarizedExperiment_1.37.0 Biobase_2.67.0 GenomicRanges_1.59.1
[13] GenomeInfoDb_1.43.4 IRanges_2.41.2 S4Vectors_0.45.2 BiocGenerics_0.53.5
[17] generics_0.1.3 MatrixGenerics_1.19.1 matrixStats_1.5.0 OmicsMLRepoR_1.1.0
[21] dplyr_1.1.4
loaded via a namespace (and not attached):
[1] ggtext_0.1.2 fs_1.6.5 bitops_1.0-9 DirichletMultinomial_1.49.0
[5] lubridate_1.9.4 httr_1.4.7 RColorBrewer_1.1-3 GenomicDataCommons_1.31.0
[9] tools_4.5.0 backports_1.5.0 utf8_1.2.4 DT_0.33
[13] R6_2.5.1 vegan_2.6-8 lazyeval_0.2.2 mgcv_1.9-1
[17] permute_0.9-7 withr_3.0.2 TCGAutils_1.27.6 gridExtra_2.3
[21] cli_3.6.3 textshaping_1.0.0 formatR_1.14 sandwich_3.1-1
[25] slam_0.1-55 mvtnorm_1.3-3 readr_2.1.5 rapiclient_0.1.8
[29] Rsamtools_2.23.1 systemfonts_1.2.1 yulab.utils_0.1.9 foreign_0.8-88
[33] stringdist_0.9.15 scater_1.35.0 decontam_1.27.0 parallelly_1.41.0
[37] readxl_1.4.3 fillpattern_1.0.2 rstudioapi_0.17.1 RSQLite_2.3.9
[41] BiocIO_1.17.1 visNetwork_2.1.2 vroom_1.6.5 rbiom_2.0.13
[45] Matrix_1.7-2 futile.logger_1.4.3 ggbeeswarm_0.7.2 DECIPHER_3.3.2
[49] abind_1.4-8 lifecycle_1.0.4 yaml_2.3.10 RaggedExperiment_1.31.1
[53] biocViews_1.75.0 SparseArray_1.7.4 BiocFileCache_2.15.1 grid_4.5.0
[57] blob_1.2.4 promises_1.3.2 ExperimentHub_2.15.0 crayon_1.5.3
[61] miniUI_0.1.1.1 lattice_0.22-6 beachmat_2.23.6 GenomicFeatures_1.59.1
[65] KEGGREST_1.47.0 pillar_1.10.1 knitr_1.49 rjson_0.2.23
[69] boot_1.3-31 estimability_1.5.1 lpSolve_5.6.23 codetools_0.2-20
[73] glue_1.8.0 data.table_1.16.4 vctrs_0.6.5 png_0.1-8
[77] treeio_1.31.0 Rdpack_2.6.2 cellranger_1.1.0 gtable_0.3.6
[81] cachem_1.1.0 xfun_0.50 mime_0.12 rbibutils_2.3
[85] S4Arrays_1.7.1 reformulas_0.4.0 RTCGAToolbox_2.37.2 DiagrammeR_1.0.11
[89] bluster_1.17.0 nlme_3.1-166 bit64_4.6.0-1 filelock_1.0.3
[93] data.tree_1.1.0 irlba_2.3.5.1 vipor_0.4.7 rpart_4.1.24
[97] colorspace_2.1-1 DBI_1.2.3 Hmisc_5.2-2 nnet_7.3-20
[101] tidyselect_1.2.1 processx_3.8.5 emmeans_1.10.6 bit_4.5.0.1
[105] compiler_4.5.0 curl_6.2.0 rvest_1.0.4 httr2_1.1.0
[109] graph_1.85.1 BiocCheck_1.43.2 htmlTable_2.4.3 BiocNeighbors_2.1.2
[113] xml2_1.3.6 DelayedArray_0.33.4 rtracklayer_1.67.0 checkmate_2.3.2
[117] scales_1.3.0 RBGL_1.83.0 callr_3.7.6 rappdirs_0.3.3
[121] stringr_1.5.1 digest_0.6.37 minqa_1.2.8 rmarkdown_2.29
[125] htmltools_0.5.8.1 pkgconfig_2.0.3 base64enc_0.1-3 lme4_1.1-36
[129] sparseMatrixStats_1.19.0 dbplyr_2.5.0 fastmap_1.2.0 rlang_1.1.5
[133] htmlwidgets_1.6.4 UCSC.utils_1.3.1 shiny_1.10.0 DelayedMatrixStats_1.29.1
[137] farver_2.1.2 zoo_1.8-12 jsonlite_1.8.9 BiocParallel_1.41.0
[141] BiocSingular_1.23.0 RCurl_1.98-1.16 magrittr_2.0.3 Formula_1.2-5
[145] scuttle_1.17.0 GenomeInfoDbData_1.2.13 patchwork_1.3.0 munsell_0.5.1
[149] Rcpp_1.0.14 ape_5.8-1 ggnewscale_0.5.0 viridis_0.6.5
[153] stringi_1.8.4 zlibbioc_1.53.0 RJSONIO_1.3-1.9 MASS_7.3-64
[157] AnnotationHub_3.15.0 plyr_1.8.9 mediation_4.5.0 parallel_4.5.0
[161] ggrepel_0.9.6 splines_4.5.0 gridtext_0.1.5 hms_1.1.3
[165] ps_1.8.1 igraph_2.1.4 RUnit_0.4.33 reshape2_1.4.4
[169] ScaledMatrix_1.15.0 futile.options_1.0.1 BiocVersion_3.21.1 XML_3.99-0.18
[173] evaluate_1.0.3 lambda.r_1.2.4 BiocManager_1.30.25 httpuv_1.6.15
[177] nloptr_2.1.1 tzdb_0.4.0 rols_3.3.0 tidyr_1.3.1
[181] purrr_1.0.2 ggplot2_3.5.1 BiocBaseUtils_1.9.0 rsvd_1.0.5
[185] xtable_1.8-4 restfulr_0.0.15 tidytree_0.4.6 later_1.4.1
[189] viridisLite_0.4.2 ragg_1.3.3 tibble_3.2.1 GenomicAlignments_1.43.0
[193] memoise_2.0.1 beeswarm_0.4.0 AnnotationDbi_1.69.0 cluster_2.1.8
[197] timechange_0.3.0 mia_1.15.6