Message-ID: <BL1PR12MB530119C9B3499641F93181B2F941A@BL1PR12MB5301.namprd12.prod.outlook.com>
Date: 2026-03-17T10:53:31Z
From: Shepherd, Lori
Subject: [Bioc-devel] help with GENESIS failing build on kjohnson3
In-Reply-To: <20260307110237.466da1a9@Tarkus>
Kjohnson3 has the updated data.table. The issue is the missing reverse dependencies. It looks like its stemming from the error in gdsfmt, that prevents the other packages from being available. When gdsfmt is available this should resolve.
Lori 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 at r-project.org> on behalf of Ivan Krylov via Bioc-devel <bioc-devel at r-project.org>
Sent: Saturday, March 7, 2026 3:02 AM
To: Stephanie Gogarten <sdmorris at uw.edu>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] help with GENESIS failing build on kjohnson3
Dear Stephanie Gogarten,
? Fri, 6 Mar 2026 16:22:27 -0800
Stephanie Gogarten <sdmorris at uw.edu> ?????:
> GENESIS is failing on the mac builder kjohnson3
> <https://secure-web.cisco.com/1uxWopRUKGxrKty-9E3pPdLzEQDXKQTYACla6wKF6BgqgXazR2N4PJupr5lMQ37fW6Y_FxJoZnOOKvf4xP-nwcdwgXCoJXkYjHYTQE2oAVo1gtbsP9AvqgZcgyLHzP1-V97g0GVH72m2Set0RcA3008f2ZATAfEX0B2T5_NS9yDYAu8w90a7HObdxTRCX05O7IjQB0NHSa-T7zUZzF5bzC-rGOMIAzaPoMTPnG5dJXtkZt-hyX2f1AjcjW22J2O-P8qUejuvGIxoGkWCcypW7IWm_jrHu1CL3U_hohOG3Et41nNn0lSkyTDubgwEHmEG40qVCY8DHdbgaZEurEy_Fqw/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FGENESIS%2Fkjohnson3-buildsrc.html>
> with an error that I don't understand.
>> Error in `[.data.table`:
>> ! attempt access index 3/3 in VECTOR_ELT
>> 16. x[, `:=`("allele.index", seq_len(.N)), by = "variant.id"]
>> 17. data.table:::`[.data.table`(...)
The macOS builder 'kjohnson3' has data.table version 1.17.8 installed
[*]. The 1.17.x series was increasingly incompatible with R-devel,
which we only fixed in 1.18.0 (and then fixed again in 1.18.2.1). This
is one of those problems:
https://secure-web.cisco.com/1chZlsCjLutNlUFn5guBKWRqc-uITeUAaeE3i8QmQHJfxDNa-Aeq2fvwKyVir54tPHIK7B8w6pKg185Yi1UpiHnWTLv2SR6WIduKvGfQoyUMw3Mi1Z3nV2P0jwpzzOx9JpENSqnyCZATW2g5OUnXrZUT6Lv19tkYctlaZvXFidlsQbgg7bysX8DVrmdZw_5w4ppaLFzEAfMvP6wo2wBh3b3Prkvf3T7QI018XqzIdGXvNNG-Fm9jaXGwN2GslE0eUnh1PdapC-mw0hw6MfdNk6BCc_5w1eYlQbHYNkUOed2iKQ0pcc6AVHt4ImL_h7ZSMkmLdcVR5tCB3nXB6KXE0gA/https%3A%2F%2Fgithub.com%2FRdatatable%2Fdata.table%2Fissues%2F7486
Installing data.table 1.18.2.1 from CRAN on kjohnson3 should fix the
problem.
--
Best regards,
Ivan
[*]
https://secure-web.cisco.com/19NaiPRdzf_7C6PyXW-zg4fi1gs9oDBCmK5BSr-3sRyrAjEJ78V9XI4rBtU1lOwCARBPdNzrfLJB1rZbEc56ePKfvnKAmx6UbShoBVd-WYi8iIhiWh6NwyPofT2chDHCv5HBnqu0CLtT9pdRni9NzZb0r2SnX5QZJmOW3m4owLJq5n_lQCLCXqiEVD8YPmrFSz6idlSnuCn53VZcj95IZduuFhjL0cejiHqVpzJPSi1IRQSLtqOrMcH3H-jLpThz9EeB2w493amXdDYgTmlpyVhd3UjwqJmq64eTu-p8AOEeEWu9aNUocb18usHTnMoZLRbXg9g_pyc23w4hl36OGuA/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fkjohnson3-R-instpkgs.html
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