[Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21

Tue Dec 3 17:17:32 CET 2024

You could just grab Sean's version from his GEOquery GitHub and put the function in your package.

https://github.com/seandavi/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7

Best,

Jim

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Zhu, Jack (NIH/NCI) [E] via Bioc-devel
Sent: Tuesday, December 3, 2024 10:39 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21

Thanks, Lori. I will work on it. Any suggestions from others will be appreciated.

Best,

Jack Zhu

From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Date: Tuesday, December 3, 2024 at 10:30 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>, Zhu, Jack (NIH/NCI) [E] <zhujack using mail.nih.gov>
Subject: Re: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21 gunzip function was removed from GEOquery. See https://urldefense.com/v3/__https://code.bioconductor.org/browse/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7__;!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTL3y8Jvpw$ 

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 using r-project.org> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel using r-project.org>
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel using r-project.org <bioc-devel using 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 using bioconductor.org <BBS-noreply using bioconductor.org>
Date: Tuesday, November 26, 2024 at 12:02 PM
To: Zhu, Jack (NIH/NCI) [E] <zhujack using 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://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-install.html__;!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTIHXvO_OQ$ <https://urldefense.com/v3/__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__;JSUlJSUlJSU!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTIKsuO0gQ$ ><https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-install.html*3Chttps:/*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*3E__;JS8lJSUlJSUlJSU!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTIvPaUx4g$ >

  o ERROR for 'R CMD build' on nebbiolo1. See the details here:
      https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTJVS-02Ow$ <https://urldefense.com/v3/__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__;JSUlJSUlJSU!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTJ1e8HlfQ$ ><https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-buildsrc.html*3Chttps:/*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*3E__;JS8lJSUlJSUlJSU!!K-Hz7m0Vt54!jBtCJXhmhJEDcQAiAP45dJzoYqZW2FW70K4PjgszTZwNnNX3nkBm_tiuIjIDgidtrl010iG2ak0lfTIUfmsc8w$ >

Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org

Notes:

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