[Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21
Thanks, Sean and all, for the fix. I have updated both devel and release versions. Hopefully, the error will be gone in the next build process. Best, Jack Zhu From: Sean Davis <seandavi at gmail.com> Date: Tuesday, December 3, 2024 at 11:36?AM To: Kern, Lori <Lori.Shepherd at roswellpark.org> Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>, Zhu, Jack (NIH/NCI) [E] <zhujack at mail.nih.gov> Subject: Re: [Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21 Sorry, all, for not getting to this sooner. R.utils::gunzip() is a replacement. I created PRs for those changes, but I didn't test them. Let me know how it goes. Sean
On Tue, Dec 3, 2024 at 10:31?AM Kern, Lori via Bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> wrote:
gunzip function was removed from GEOquery. See https://code.bioconductor.org/browse/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7 So you will either have to find a replacement function or implement your own. 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: [Bioc-devel] FW: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: [Bioc-devel] FW: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21
Hi,
I have been trying to fix the following error from the SRAdb building process at Bioconductor servers:
* installing to library ?/home/biocbuild/bbs-3.21-bioc/R/site-library?
* installing *source* package ?SRAdb? ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ?gunzip? is not exported by 'namespace:GEOquery'
Execution halted
ERROR: lazy loading failed for package ?SRAdb?
* removing ?/home/biocbuild/bbs-3.21-bioc/R/site-library/SRAdb?
Can you give me some suggestions?
Best,
Jack Zhu
From: BBS-noreply at bioconductor.org<mailto:BBS-noreply at bioconductor.org> <BBS-noreply at bioconductor.org<mailto:BBS-noreply at bioconductor.org>>
Date: Tuesday, November 26, 2024 at 12:02?PM
To: Zhu, Jack (NIH/NCI) [E] <zhujack at mail.nih.gov<mailto:zhujack at mail.nih.gov>>
Subject: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21
[This is an automatically generated email. Please don't reply.]
Hi SRAdb maintainer,
According to the Multiple platform build/check report for BioC 3.21,
the SRAdb package has the following problem(s):
o ERROR for 'R CMD INSTALL' on nebbiolo1. See the details here:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-install.html<https://secure-web.cisco.com/1AN4ZyYCv_R-nyMNRb7vc_mJo0zHixK_bK89bZoIGXUAYVJSMhCNMSqX0qp4BYFJm9jJU8tmYI_opDMRrCYAhuuAsrjF7tcY7kMmVGmPFKZLKGnfRIqYZX921k4VYbNH0nN4aBhMt7gH4FcYIuNeDNgmXPYbyhhHHSTq4Exo-Uo5XaMuoxQbXqnE-Ut7FEYHo03myzvwIBUAKmznyQeGeBoBlpn5dpnDfnMhB9_n1tkTpzTIP9b4uv7pi2A-pq0gh28ullTZC6B7e2JABv3FeDbC5_3MPOutDdrl4sS-Ok6-fyC79NziGX9VYqpIW4d9b/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-install.html>
o ERROR for 'R CMD build' on nebbiolo1. See the details here:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-buildsrc.html<https://secure-web.cisco.com/1ZzGNu4CautDm4WowVnXhIbwiejsZcZQAdhkTVxt6M5TFsYtpqwUyyRbEZ1Hqdey_3HRbb2xjbjYG9orwW6xHV59kVvYuF_Q1Fz5Dj7iHHwGXcbOewrQHpaUrQFB3dzYKlYljBEVr-n3cAzyw4WfjQKU1Gq1GhnbXOMZ7zoH_pVxl4LsfuM7d0MhdXxbzeBj6koYRY8qnqN7AV4YtvE2b8Rs_2pRQeoSqYNJ1nh8787JPKk3_GT1P9l0mr9YwFqx_W6YqtI-Qj4kelqZpupiUevxG9YSgkD348eUSlBJBE7d1E7EXCu41DjEC-gFaV0hP/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-buildsrc.html>
Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org<http://git.bioconductor.org/>
Notes:
* This was the status of your package at the time this email was sent to you.
Given that the online report is updated daily (in normal conditions) you
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