[Bioc-devel] orthogene: killed while reading tree

[Kern, Lori]

I'm not sure what caused it but it looks like it was intermittent as the build report is now showing all OK


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 Brian Schilder <brian_schilder using alumni.brown.edu>
Sent: Wednesday, April 5, 2023 11:38 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] orthogene: killed while reading tree

Hi everyone,

After some pushes upstream to my package orthogene<https://secure-web.cisco.com/1Yjb8CppSzUQLL9b4g0UKktihh2zFG4EoIIlbHKDWimE74owMrRVZqfccfH6b6mlcXJM6WIMD1ky8R7i1SSDiQtMOhngidorvykSLnMFZe4JfwikVDy_vAgZEClSdDvXZ5r4pufS5sdlwMA9Qa-rcNWI840cXML6--QWyOkJL63HFirIP8e6VEQCc7Td0hTZVdvWxk35kUefwA2tMRpI91HBtAzq41R5plUEPirBmX8V6-ruxxXoovFLQX2KtSiBYYdAQywGETgUmneU2meMszfNznjaGGctBiEoqp0vKTEJcIShWkwb5CB4xyPhZlKUf/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Forthogene.html>, I noticed that the release version (3.16) is failing on the server because it was �Killed� midway through. But I can�t see any details that explain why or how it was killed.
http://secure-web.cisco.com/18Y3DECHiDC5IXa6V20ApXvuSZui_k5W0qRUurD8cIzo1s_tU4g0PaicLe-0r8LHwu3VZbmQiiVjchuut0peSTNIVSRnlU1BlwfMhO6gjN5cEyhS_NrneB8jvwInNp1g7lEcjhCaKJErCeqoe3Wso3fF3umsRXS59r0mr7jZh2rtiX09STqqFOPqHnUAkzU1v8RPyWzhNUXeQcjh1K3NjY1t36KGSJrQQfTiMEir4xA2DTUIuqNRJ2BTNrW5EuH0ZwAvRVtu6Q4fuMnJlZe-mnqaYb2kSB-1kIOF9rmVBww7MJlZgjZ6983-Yk000ZZcX/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Forthogene%2Fnebbiolo2-checksrc.html

The only thing I know is that is occurs at the step where a large tree (147k species, stored as a 5.3Mb newick file) is being read into R with ape::read.tree
https://secure-web.cisco.com/1VcNDK1HHX4nN8aCtV1oJXg6ITjMsrslJ_ob2tF0xAf_ornVpQsz8BEZgdgXbjx6ahY5JLkAyjeKEkvi9jcHIB4ABv2o9ujffCFuzDGgrFpUqIBguEH7vyNAlMcdYPP6u7qmkfMxAi4E5FE0Rx_fr5VJwgjZF1A6CAHp_ICHt0vmZLVgWF6kwH0ccMywWVeORPIB0-tSbghUIGCTthFCWPrq37AO0c5_8daQxHMULHWvzWYBuUPqJtLdE48857YZpmpyGcsYbT0BrtehIMfLIrUN9_Sh2M730GTNMZc9OOK3YIFIixgDrAJNggS59lX3o/https%3A%2F%2Fgithub.com%2Fneurogenomics%2Forthogene%2Fblob%2F4e41e6322507a929562fc77cbdc602bc084a34bf%2FR%2Fprepare_tree.R%23L115

Oddly, this same code seems to work fine on devel (3.17):
http://secure-web.cisco.com/1YEyAnMymly7DaE-8T-tfgtB3qaqjFRTB_3mLcEGYfiOfGuAH8cgluekNz2bRilm8pL0EgzYXlvk-5HjyoGa8gYcJpNldgRcyJVve6ww4p3cycwTGCphRKaQou6dhBQEFws6vWDMAlWn7-2MVOdVUxQpKjbO4d7rfBVaPdyncGiMbLVRuQ7VOamFzUImU1Q_9telrakGN9oWFBWD0SFnHvi0fuaW4v4BgOxfi9kTM7Ay-J9pSibYJLBrPVmBQqoKVfgMwtR-RWWNhNA06UxGm2r-hmMJHE4Og_2QjVanrXJ7bmMwW0QI77agDy8iuyrmw/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.17%2Fbioc%2Fhtml%2Forthogene.html

Anyone know why this might be?

Thanks in advance,
Brian
___________
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | https://secure-web.cisco.com/1hSOEYYcneirgbSg4StL0qPT_AWA2F3h51iHm6FkI8XCE6gBpC8qDzdXXRCFrwV_SeVhexavZ4rKpwe3i1fs7fweCXXLkafQpyXgPKm9L63OI3NKAVxgE-0IN1cJomDWrfuDmluCu0zKa6ktv7pW_g924CbTGVKhq_Fc6rntFKZgw22zzGpnHbtYd0rRJ0WNeb3TLdCmpOfvzw9Ins21jedSRHlV1R_UN00eUYInXzJ3A0i_atvXJHt4U7_ZkRQ9FMPyn4_JKfvV4E0SGs1HCjlOteW3w30Ktpee_ELN6ZB0LILwWsWEcb8O4GXN7wkPQ/https%3A%2F%2Fbschilder.github.io%2FCV%2FCV<https://secure-web.cisco.com/1e6XskBMnzPAa3y8j3Rbpm1sSG7wFVl6ssqAlVf1gXx-lXVDbJhZV7eR56sxDvzn2P6q87KXJd7IvvwyVfttAh-oAWFRnwe6PIRd9wJyFu9i9HIhGoRQdY6BGuEPP9B_8Xm4zEhtCme9MoeVqiXmy__N338kxOqxWNh1C2mV4q96m4mc5NDByEdJUd1jJtZ5IT5nu9hO76GxvTQ67gqhSFrKxhU718FnzJMW2r8kNyEov1JbIxwYJx4sc6D5wAvbBem_ywYBO4DkNJxsAzvk_Qwl-Gvw1L6r1-LpoHQsoMhQynbR_hV9NApPXLi05YzzN/https%3A%2F%2Fbschilder.github.io%2FCV%2FCV.html>
LinkedIn | linkedin.com/in/brian-schilder<https://secure-web.cisco.com/1YTWdXOlm5Jz9ktnd_wUI-_lnO3O6CFzSRViiOuD4Z9ydjrqNodQ0H_IFqp8YhyGt6arD6On-fp5xVjaduYSTDdEKT5V6kLuq2ZBNgj992Nj6ztG_BdaV9jmhaEfqH-Rp8XMj1IBMtInGJMVfDgXreFDWbjSZGVg99PYPjtC0--lvqCJyBIrSS0CjTVE9jWnM_StyEVD8OtwQ49zw9ZnJQ8BSNxDMJ6euu1fQg1_U9DeQXj4GkNhV8D6z_6m2Pcflwh6WfwOnX31wUIsyCXMzeDGD80poj40CQU4n1uk1UmDIMQx4HEba6D4lI-ky8zcl/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fbrian-schilder%2F>
Twitter | twitter.com/BMSchilder<http://secure-web.cisco.com/1y1hyqSVBJ3tt7wTys5M5MskSuRAa_xLdiH9E9HZ2OY1Bn08XLJ2DFO53M-RucK5w2U9cJsn6XQlnDt96gnu_N7_RTgvzBYeiWJsm88xmMkEtfSWtw8kFlAox2UJV-CsHXn0Q1Z3hxe3sJ5iSFLhVu1JjoEiQWEyXVc41sIMz343H6dpKqLxOH8uWXqUbP23OwjsbXb0VJmkyKaf9HHwGXmgKVktKK5_bqRt-UwRFxsjJbrEzgTkPcbwlrwQqzkaFU2pytD9bhvnu2sWVM0B0qz-SW7jz2XLfGOmEE2j4OV0sXKnDuNKaWpYHHUJHE3CR/http%3A%2F%2Fwww.twitter.com%2FBMSchilder>
Lab | neurogenomics.co.uk<http://secure-web.cisco.com/1_gWEl4VLEAB6Pau8JeqtqYnEsfCLmjC6sIachNZZZxStN6HwXgn2AmZ5biggCHL3YRDcrehKAgJuvsXqolrXQu4NL0idG21yszcnfJj10IgtuQ9IDcgcr8gUtAqwdUyUs-2AVm9xD2t1hQJVDSJ_FO8zy5K7fbxTBr_Jh4cyXwDRX_2GSUEHKEN_0nD8Mfbnr5hA9IN_A-Rp5VYGxy9bu7nZzzEVTfxAJEcv_XY_9SJqAmYn7Gkyoo3MseLpId158yu0mneEHz5qgIax-wq7ScS-QtV7dff19nF5DCbPr6pEAWBww8uxuTcqCO0Re-cC/http%3A%2F%2Fneurogenomics.co.uk>
UK DRI | http://secure-web.cisco.com/1zBNM9wbZUi_gC_DcViNucWxWxosXAAuN6wHp0BTsFK4Q0Ue5Xq20VyU4tLD4ewITi_rMB5JwsVcI3VT7mRFAZTSM5FpOixUeRLrjBB0uGdgpVvurhphp-y0lEZBGIO19s--6KUxT_4Hz76n-bQtS_Qc_0GiFw-5cJpOQd3Qzh8E8JG4ViLVgYY0AgsRvi-eR6fbEyJkhWTRKTglnFI7138SkIwDGwg18qBLTPXE2L7ZZ5NCDX5GcwhW3rQQ5JKWOv2bjZM4xAybiF7C23obti-oFVnGpYshFdoooOaHZU0tWVyqhEU7jQ2z3inEC8JNw/http%3A%2F%2Fwww.ukdri.ac.uk<http://secure-web.cisco.com/1ugNf2GrQi-Xtj0HfsppMWxTAXJt9AoleO1WETTn8cmPxvvnZh6arL-e96wavMM60zzzrTRFIM7D3wvua5HXnebMh3o89ksGe_VQ3KQFtPZjlKJlFSgRn8CosedNMSwqaaW66_IgdJ4lMGq52AYV2bgCV6mYz_w26A8hNTSL_MgUNh6mc3NeFz7g7Grm9XbXxr7uSzzNEcf2_VKsE4nWvBe473Tvbiqp1xKBwWYjgrhGJbg37fDoFg8YbLGzF3A1WG4yNNCkVKhXZyT5HOrfN6SYAxCzTtWMq9JfZwpW8vu99AL29hyqAcQ9p34HykCl0/http%3A%2F%2Fwww.ukdri.ac.uk%2F>

        [[alternative HTML version deleted]]



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]]