[Bioc-devel] [EXTERNAL] Re: Bioconductor package rcellminerData

Thu Nov 3 13:19:41 CET 2022

Hi Lori,

The package rcellminerData did not bump to version 2.20.0. Is it related to the build warning? Please let me know what is the issue. And how to fix it?

Thanks,

Fathi

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Monday, April 18, 2022 at 9:16 AM
To: "Elloumi, Fathi (NIH/NCI) [E]" <fathi.elloumi using nih.gov>
Cc: Hervé Pagès <hpages using fredhutch.org>, bioc-devel <bioc-devel using r-project.org>
Subject: [EXTERNAL] Re: Bioconductor package rcellminerData

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Experiment Data packages are built every Tue and Thur.  as shown on the build report header page http://bioconductor.org/checkResults/<https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2F&data=04%7C01%7Cfathi.elloumi%40nih.gov%7C65e2553eb36a4943fe1608da213daaad%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637858845986991504%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qzbjdlIMCKF%2BPNjlkmyOddWtpRnzQdApp%2FQH7HJq4MY%3D&reserved=0>

The changes pushed up last Thur 14 would have been too late to be included in a Thursday build report.  I expect the changes to be visible after Tomorrow's build report posts.

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Elloumi, Fathi (NIH/NCI) [E] <fathi.elloumi using nih.gov>
Sent: Monday, April 18, 2022 9:12 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Hervé Pagès <hpages using fredhutch.org>; bioc-devel <bioc-devel using r-project.org>
Subject: Re: Bioconductor package rcellminerData

Hello Lori,

I bumped the rcellminerData dev version from 2.17.0 to 2.17.1 since 4/14 and I did see it on devel builders: http://bioconductor.org/checkResults/3.15/data-experiment-LATEST/rcellminerData/<https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsecure-web.cisco.com%2F1s-iF2UYBJfYCAfGpCmXbWtJhQFybcrBDIVxYSViZrfDLNHBXH6DOqbL9SFxE3YpBywTkE5GNGS1al6M2DDdPQj1fhH8WpjDdMSge4G2HOwp0bJADAn2fSAvYL1NnzzXdu-AjPk3XlzGcFqB71OXS0JBBxr5OFPY30Go-8f4YKkKRsjo-26qrybURbKFPP0i6RvSExG0YYwi1uHja2cKzF_PcEGo7vEpGBjRLGufwLFyTjmpp-uo7Nt2odBO3OwbPB2PXgv6_p2uau4wSaYkuNGZ6BKgklD_47sgTO_h-oucpA1ln1adMzYXCbrE5OzFq%2Fhttp%253A%252F%252Fbioconductor.org%252FcheckResults%252F3.15%252Fdata-experiment-LATEST%252FrcellminerData%252F&data=04%7C01%7Cfathi.elloumi%40nih.gov%7C65e2553eb36a4943fe1608da213daaad%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637858845986991504%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=f99SXrtHkGNLwTr0mycvZlRZelQS%2Fwvg1UaPeKx4FSg%3D&reserved=0>

Could help me with this issue?

Thanks,

Fathi

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Tuesday, June 29, 2021 at 10:50 AM
To: "lunaa using cbio.mskcc.org" <lunaa using cbio.mskcc.org>, "Rajapakse, Vinodh (NIH/NCI) [C]" <vinodh.rajapakse using nih.gov>, "Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi using nih.gov>
Subject: Bioconductor package rcellminerData

Hello package maintainer,

We would like to bring to your attention that your package is failing on the devel builders of Bioconductor:

http://bioconductor.org/checkResults/3.14/data-experiment-LATEST/rcellminerData<https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsecure-web.cisco.com%2F1wTHb4J5vYt79t1m8zlFtYsm9GvIk_ERR_mIiz8DJ7FKPtWOrlHAMPFSIg9IJNrdx4yDn72YFxwEA2JLKY-yrddpSDKVmIwZKNbMfxBnZBsZJv9jUiV2JzZ3KGALeIW4nOObhPYbxDjjaD1Ee8HymsDdkkQ88v5MwhPXJyf_QPTmsUxJNvj7j1OI7G8t0ZohewDr43q6cQ0aGQ7d_VQQeoRf_Km-v1cWRJBH0TQqxj0iRjn_LdKla1rB3zAvE_n9D-etgmJXwm7hZEomnbN40wUMGfwWg_5w7GXN1mzAicTaHOwVs5mqdd1iXkWPoXqxt%2Fhttp%253A%252F%252Fbioconductor.org%252FcheckResults%252F3.14%252Fdata-experiment-LATEST%252FrcellminerData&data=04%7C01%7Cfathi.elloumi%40nih.gov%7C65e2553eb36a4943fe1608da213daaad%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637858845986991504%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GFVis7Hpr8yjv%2FUN678SKAp%2Fc0cto6EWNluHMa8jSD0%3D&reserved=0>

Please fix your package as soon as possible. If the package remains broken for an extended period of time, we will deprecate the package.

The ERROR results from an update in the knitr package as announced here:

https://stat.ethz.ch/pipermail/bioc-devel/2021-June/018223.htm<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web.cisco.com%2F1dwHEjF3CCkUF9mhzYvELi0IoERCWPTDzCNUl4bPe8QHKf5aWv9Qj7RinMoAinXfZQvzIbamMr9vgVmcKdKentGLNBYnF2icPuu6W6_BL5oPPpiMgeN75gzr7wVSN9HVhgO93pdFjVPQP0JuYPlQ2bB4Dik9A4Q20nYCBe4Bd4tDAQvTN1GbdpgPgLrBMRFNYqgqajL57mzfzHHN8dg-jexyKc1H3rYdb1_uRMdKdYWnvIEw-vql288A4M3FJnSNcLPgtSljKQUrif5aUsoGTLc2rUrxs19wMcq0jf79X5HrQe6d4TQatb84HbMxl2_az%2Fhttps%253A%252F%252Fstat.ethz.ch%252Fpipermail%252Fbioc-devel%252F2021-June%252F018223.htm&data=04%7C01%7Cfathi.elloumi%40nih.gov%7C65e2553eb36a4943fe1608da213daaad%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637858845986991504%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JIvqVRnx5%2FNZM%2FYMdArU0EnEsSN4sW37pZk9sO26hGs%3D&reserved=0>

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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