[Bioc-devel] Error during download data by GDCquery_clinic

[Kern, Lori]

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-bounces using r-project.org> on behalf of Jaros�aw Sikora via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, March 3, 2025 10:16 AM
To: bioc-devel using r-project.org <bioc-devel using 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: jsikora using ibch.poznan.pl

wewn.: 1194 | pok. 226, B

                  [2]  [3]  [4]  [4]



Links:
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[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
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