[Bioc-devel] help with GENESIS failing build on kjohnson3

[Andres Wokaty]

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 using r-project.org> on behalf of Kern, Lori via Bioc-devel <bioc-devel using r-project.org>
Sent: Tuesday, March 17, 2026 6:53 AM
To: Stephanie Gogarten <sdmorris using uw.edu>; Ivan Krylov <ikrylov using disroot.org>
Cc: bioc-devel using r-project.org <bioc-devel using 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 using r-project.org> on behalf of Ivan Krylov via Bioc-devel <bioc-devel using r-project.org>
Sent: Saturday, March 7, 2026 3:02 AM
To: Stephanie Gogarten <sdmorris using uw.edu>
Cc: bioc-devel using r-project.org <bioc-devel using 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 using 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$

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