[Bioc-devel] help with GENESIS failing build on kjohnson3
I've updated kjohnson3 and was able R CMD INSTALL and build gdsfmt. We should see it on the report this weekend or Monday. Andres Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kern, Lori via Bioc-devel <bioc-devel at r-project.org>
Sent: Tuesday, March 17, 2026 6:53 AM
To: Stephanie Gogarten <sdmorris at uw.edu>; Ivan Krylov <ikrylov at disroot.org>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] help with GENESIS failing build on kjohnson3
Sent: Tuesday, March 17, 2026 6:53 AM
To: Stephanie Gogarten <sdmorris at uw.edu>; Ivan Krylov <ikrylov at disroot.org>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] help with GENESIS failing build on kjohnson3
* External Sender - Proceed Cautiously with Links and Attachments. * 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://urldefense.com/v3/__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__;JSUlJSUlJSU!!LRXxDv2l!UDncoDbn75OrJg6Ol-KEupgwvw2LeJYjPXLBqji5AU2LzYA_aDzfZzuGV3eDyhtz7N47LHjtkitGSP8hk1ztCk90dklnFuXU5Q$ > > 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://urldefense.com/v3/__https://secure-web.cisco.com/1chZlsCjLutNlUFn5guBKWRqc-uITeUAaeE3i8QmQHJfxDNa-Aeq2fvwKyVir54tPHIK7B8w6pKg185Yi1UpiHnWTLv2SR6WIduKvGfQoyUMw3Mi1Z3nV2P0jwpzzOx9JpENSqnyCZATW2g5OUnXrZUT6Lv19tkYctlaZvXFidlsQbgg7bysX8DVrmdZw_5w4ppaLFzEAfMvP6wo2wBh3b3Prkvf3T7QI018XqzIdGXvNNG-Fm9jaXGwN2GslE0eUnh1PdapC-mw0hw6MfdNk6BCc_5w1eYlQbHYNkUOed2iKQ0pcc6AVHt4ImL_h7ZSMkmLdcVR5tCB3nXB6KXE0gA/https*3A*2F*2Fgithub.com*2FRdatatable*2Fdata.table*2Fissues*2F7486__;JSUlJSUlJQ!!LRXxDv2l!UDncoDbn75OrJg6Ol-KEupgwvw2LeJYjPXLBqji5AU2LzYA_aDzfZzuGV3eDyhtz7N47LHjtkitGSP8hk1ztCk90dkm2GjFSUA$ Installing data.table 1.18.2.1 from CRAN on kjohnson3 should fix the problem. -- Best regards, Ivan [*] https://urldefense.com/v3/__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__;JSUlJSUlJQ!!LRXxDv2l!UDncoDbn75OrJg6Ol-KEupgwvw2LeJYjPXLBqji5AU2LzYA_aDzfZzuGV3eDyhtz7N47LHjtkitGSP8hk1ztCk90dkn_blX1Cw$ _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.com/v3/__https://secure-web.cisco.com/1rl1iFSvhrl4a1BQOY-qArnvGMY97eXnso3EmFQrdYvu9UDKpezIZPxVt4gdEPFZFd7ck3Joyj8pZT_fu-eQzemSeXZ1-hYcEgzVnKaFV6L57sjEZQm-BXB9nFqvIjOSeHH_AnqmruGAW5dSu3aIzpaxVJWvlb8Ra18jq62xOVcxbP6Db7oQwiwQEA7d56FXMH2ZmX9oLYRWskL8271C3YLKvue-g7e-ndDZRD7toIfgix_4t2K5QfK5mEBQCZ_x_edA7TSjSndTTkff85X8F8tCJQ0HYDgQK4-1CoURO8PWoC-OyrWumXBpUk8jdk8L-IRTq3U84t068NzgXg7Nvaw/https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fbioc-devel__;JSUlJSUl!!LRXxDv2l!UDncoDbn75OrJg6Ol-KEupgwvw2LeJYjPXLBqji5AU2LzYA_aDzfZzuGV3eDyhtz7N47LHjtkitGSP8hk1ztCk90dklIF-IEKA$ 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]]