It looks like a bug in the code that was fix in devel but not pushed to release (assuming you are using Bioc 3.20 / R 4.4? as you did not provide your sessionInfo?)
We will ask the maintainers to fix the release version. While its not recommended to install from outside BiocManager::install to prevent mismatch and incompatible versions, you could install the updated github branch directly from the maintainer of the package in the meantime: library(devtools) devtools::install_github(repo="BioinformaticsFMRP/TCGAbiolinks", ref="devel") Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jaros�aw Sikora via Bioc-devel <bioc-devel@r-project.org> Sent: Monday, March 3, 2025 10:16 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] Error during download data by GDCquery_clinic Hello, I have problem with GDCquery_clinic available at https://secure-web.cisco.com/1XME7XiYaGoJLaBkuhZ7kVxkHzy_hKpvepu1dnkFDLgyDMaelOPt-jfXyHz4spsk8gePRDcXqD26h9ie3EvI0yTcudA1jLhfnLjZSRrNvc1QrMlUQLxryENIrRdhHnaZkEm6jEmUUO0qmPsAkxsnv8ZoSjev8MvVsMhjC2Dvo4q__u-xW32ITRnPqURUdwoRY3PkS-gM0wosRRsN2tYP7p1IXTn7ZVxq4wfz2EIWEVvJR363Cf72DaCSWjSD0a0bpWLCzntGGrColCiDnamVGchksQ4-q5JKEAHMM3VAJxP8dV85BslCd6_MQ1YllebrN/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fvignettes%2FTCGAbiolinks%2Finst%2Fdoc%2Fclinical.R . When I tried used command: q1 <- GDCquery_clinic(project = "TCGA-OV", type = "clinical") I got error: Error in set(x, j = name, value = value) : Supplied 608 items to be assigned to 1130 items of column 'submitter_id'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code. Could you help me? Regards, Jaros�aw Sikora -- Pozdrawiam [1] mgr in�. Jaros�aw Sikora | Specjalista bioinformatyk Zak�ad Biologii Molekularnej i Systemowej Instytut Chemii Bioorganicznej Polskiej Akademii Nauk ul. Noskowskiego 12/14 | 61-704, Pozna� email: jsik...@ibch.poznan.pl wewn.: 1194 | pok. 226, B [2] [3] [4] [4] Links: ------ [1] https://secure-web.cisco.com/1wanu0P9eWOrpIcWclN_F5WAeSrg3VhhaZWDHqjKYFBUJGJK7342RVv2vYpUfvZlwJmIwt4cZWQuGO3VR_eRHxbZ1C-tC82RNKTzlGNyM_7gmclfCNL6EZLbTPNGNU1qVWJzqBjR5CyA3MO0NPN-Ba-mytaO1pLZeJ5pdMLcXGdlbeGm13AKgz_bm-fYzNqFxCdd83WT9-X4hCBHMJRSxavbgM7kqjpF9XBGeppGLwwX_83VCOuqEc3S37CECB307KncsvpwDk-zrxhJZ9r19Q13a2Nn-p8FxrWE4_ZjZbWV6jeaE_jPbOSI3c2pa5SQE/https%3A%2F%2Fwww.ibch.poznan.pl%2Fpl%2Ftop-pl%2Fhome%2F [2] https://secure-web.cisco.com/1aPNf3xI7IlRVKn9xbqE5WVM94WpDRR-6D_lB1ktVUj3Mp7vK6V0xvMFmW2sASm1veAhDudAC0VzMR8Vplg9UPNytayfivLyCjfqQkan7KeUVT1cGKC3QH2WFT6oAEce1f6AOdu1d4cgs1P1lq6PEUivYdXr8jo-NEYRPElDe13mMCFoTftaE_hxe_JMnvsJIHSlte7GYTqbg7F8OXyFOH_H_QuIYFk9jRz8187ts7HJid8p1oYY13uBVetaxBxNZ2z5a_8j7x3A-q8vjpy905lEqhCg7pzU3t1FEeIODFR7at8P06BUBYA5yX8498dlJ/https%3A%2F%2Fwww.facebook.com%2FInstytut-Chemii-Bioorganicznej-Polskiej-Akademii-Nauk-ICHB-PAN-1983068941913518%2F [3] https://secure-web.cisco.com/1dlSeW3n2Knb6pMuXLMLKF1g9m-B7tPrFSYGOVpPir-3DZQeFQdY7W9AfRJYT_UlrkdF0GeRq3-tGh2OX81mjkOOaGIRWqvxLvFrIkivHHiyoTpzzdNA7wK0x5W2Yr_5IafZPInJwjDuwTbLGKI20IJqWychLw9c_L2zrACVIMgvE8od40wFwg-xdpC9Q2E3X0HcbHqn-KzfnDtfWBl8NQ2SucX6R9nSEqgW46-64Ir5ESG48V1CNQ2lRWKyxur5LlPi6o3cSKUdt19Icc7ft4D1rHXhtt6TEfzMrJlSin1pjQNrDWzcsit98WNp3-yFW/https%3A%2F%2Ftwitter.com%2FICHBPAN [4] http://secure-web.cisco.com/1x0D5bGbYZ2nGMGmBV7ttPtir89vLUKTb0QcQmFj55l-JToxSQpedl97mYMUSkHWssVtkbyA5A3Re2iYUE09MeSOQ-UjoEh8t-ITshwpfTy8IkyrT-XBOOTXXP3sGoz95oN8pRMMvgxMhOuHarQzfa-ycQipOCprr_u2I4pPQgZI4gGQ6D-Je8v4h_RA4f36BofKBIofQ9hxg24XFzpAEGJyRQxmpE9xcb3wfZn9mogmVyVOUHY9iYnL6sBqVphbizldbLnup6wCFQYD1c4Nq5V6Ht9mhVIK2M5jhnhfXUAeoO0sn37lDeXS0ncMurI5G/http%3A%2F%2Fwww.ibch.poznan.pl [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1uY25INyxmxV-sDzSBJtGXCvsWpz7IKbop4pLxgpucCG9_JIHiw3VJ6PbneG9B8uFAur0i6fz9q3KAJrW4orlvk8SVIGpPN3rthxKdfJv6PznvDYak8zUR1Jb0VfH6zKhMQXiguL8oYiGHL09yLPBZr1WaiS_5HCS5jAy4jXPbP3tquQUeUB2_LDibhIi3-i_2rj91n7zzOtnNS8jqWUVIuqZuvW5khM-9G9Sh2kRMCW2wsJsffludB-bBXjEikzbpctljO9aV-EubhQrFkaXY-V-RAObU5nnwukY2Ak5tqt5j4hPXNP5ALU6KGFylWRH/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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