Re: [Bioc-devel] orthogene: killed while reading tree

2023-04-10 Thread Brian Schilder 
Indeed, thanks!

___
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | https://bschilder.github.io/CV/CV<https://bschilder.github.io/CV/CV.html>
LinkedIn | 
linkedin.com/in/brian-schilder<https://www.linkedin.com/in/brian-schilder/>
Twitter | twitter.com/BMSchilder<http://www.twitter.com/BMSchilder>
Lab | neurogenomics.co.uk<http://neurogenomics.co.uk>
UK DRI | www.ukdri.ac.uk<http://www.ukdri.ac.uk/>

From: Kern, Lori 
Date: Monday, 10 April 2023 at 13:03
To: Brian Schilder , bioc-devel@r-project.org 

Subject: Re: orthogene: killed while reading tree
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  on behalf of Brian Schilder 

Sent: Wednesday, April 5, 2023 11:38 AM
To: bioc-devel@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><https://secure-web.cisco.com/1hSOEYYcneirgbSg4StL0qPT_AWA2F3h51iHm6FkI8XCE6gBpC8qDzdXXRCFrwV_SeVhexavZ4rKpwe3i1fs7fweCXXLkafQpyXgPKm9L63OI3NKAVxgE-0IN1cJomDWrfuDmluCu0zKa6ktv7pW_g924CbTGVKhq_Fc6rntFKZgw22zzGpnHbtYd0rRJ0WNeb3TLdCmpOfvzw9Ins21jedSRHlV1R_UN00eUYInXzJ3A0i_atvXJHt4U7_ZkRQ9FMPyn4_JKfvV4E0SGs1HCjlOteW3w30Ktpee_ELN6ZB0LILwWsWEcb8O4GXN7wkPQ/https%3A%2F%2Fbschilder.github.io%2FCV%2FCV%3chttps:/secure-web.cisco.com/1e6XskBMnzPAa3y8j3Rbpm1sSG7wFVl6s

Re: [Bioc-devel] orthogene: killed while reading tree

2023-04-10 Thread 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  on behalf of Brian Schilder 

Sent: Wednesday, April 5, 2023 11:38 AM
To: bioc-devel@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_Jh4

[Bioc-devel] orthogene: killed while reading tree

2023-04-05 Thread Brian Schilder 
Hi everyone,

After some pushes upstream to my package 
orthogene, 
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://bioconductor.org/checkResults/release/bioc-LATEST/orthogene/nebbiolo2-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://github.com/neurogenomics/orthogene/blob/4e41e6322507a929562fc77cbdc602bc084a34bf/R/prepare_tree.R#L115

Oddly, this same code seems to work fine on devel (3.17):
http://bioconductor.org/packages/3.17/bioc/html/orthogene.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://bschilder.github.io/CV/CV
LinkedIn | 
linkedin.com/in/brian-schilder
Twitter | twitter.com/BMSchilder
Lab | neurogenomics.co.uk
UK DRI | www.ukdri.ac.uk

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