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 <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>
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://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-install.html&data=05%7C02%7Czhujack%40mail.nih.gov%7C2d8e4de407b541632f3008dd0e3c23e1%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638682373642122376%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=6jBmvRWGUP3G3XsOPOJ3SXbiz09ymPILk1uPRX5W39w%3D&reserved=0<https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-install.html>
o ERROR for 'R CMD build' on nebbiolo1. See the details here:
https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FSRAdb%2Fnebbiolo1-buildsrc.html&data=05%7C02%7Czhujack%40mail.nih.gov%7C2d8e4de407b541632f3008dd0e3c23e1%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638682373642139544%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Mwh4DMRbOTqOZX9YwoUMC5ecabklRF0eyC3iFiFeq58%3D&reserved=0<https://bioconductor.org/checkResults/3.21/bioc-LATEST/SRAdb/nebbiolo1-buildsrc.html>
Please take the time to address this by committing and pushing
changes to your package at 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
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.
* It is possible that the problems reported in this report are false positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.
* Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.
* If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:
https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F&data=05%7C02%7Czhujack%40mail.nih.gov%7C2d8e4de407b541632f3008dd0e3c23e1%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638682373642151350%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=VxLR0n3TJR74j18fPzYNUAoL3iQ66kM4a%2B9lEX1ZVDo%3D&reserved=0<https://bioconductor.org/help/mailing-list/>
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[Bioc-devel] FW: [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21
6 messages · Shepherd, Lori, James W. MacDonald, Sean Davis +1 more
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> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel at r-project.org>
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel at r-project.org <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 <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 <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>
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
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
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.
* It is possible that the problems reported in this report are false positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.
* Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.
* If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:
https://bioconductor.org/help/mailing-list/<https://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F>
(all package maintainers are requested to subscribe to this list)
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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.
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Thanks, Lori. I will work on it. Any suggestions from others will be appreciated. Best, Jack Zhu From: Kern, Lori <Lori.Shepherd at RoswellPark.org> Date: Tuesday, December 3, 2024 at 10:30?AM To: bioc-devel at r-project.org <bioc-devel at r-project.org>, Zhu, Jack (NIH/NCI) [E] <zhujack at 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://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> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel at r-project.org>
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel at r-project.org <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 <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 <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>
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><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>
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><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>
Please take the time to address this by committing and pushing
changes to your package at 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
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.
* It is possible that the problems reported in this report are false positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.
* Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.
* If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:
https://bioconductor.org/help/mailing-list/<https://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F><https://bioconductor.org/help/mailing-list/%3Chttps://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F%3E>
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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 at 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 at RoswellPark.org>; bioc-devel at 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 at RoswellPark.org> Date: Tuesday, December 3, 2024 at 10:30?AM To: bioc-devel at r-project.org <bioc-devel at r-project.org>, Zhu, Jack (NIH/NCI) [E] <zhujack at 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 at r-project.org> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel at r-project.org>
Sent: Tuesday, December 3, 2024 10:20 AM
To: bioc-devel at r-project.org <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 <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 <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>
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
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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> 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> on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel <bioc-devel at r-project.org> Sent: Tuesday, December 3, 2024 10:20 AM To: bioc-devel at r-project.org <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 <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> 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 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 could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/< https://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/< https://secure-web.cisco.com/11nfrWFeZhEfs2u-5iGvsJWvA3MvIg5RMPVjK_wuoeFG5eAW8vIaYWOyxc9KOyFlO38h3ZpYhnEKsaoEtJGl-Z6EI6qaecH0-iv8m7ZIvMIxgXnumYYjx883xa46-S0sdqc243WHosQgtbPpVZccWtVoe_VDShYo4kQ0bWZPBGW5wTHsJ-tAvLl0hL4ldXN-I-O27gwYUEAZ55mWzY1bScI47CcKs4hs3nCHURypmtn4kWRYrRc_vJ1HmR6Ty-LORtRl7qB0CZa4_dveTtGC7SNcOMY_ujow9sHx2RpogMfHXRO7sVq1To8SAoYqA1KIR/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Frss-feeds%2F Thanks for contributing to the Bioconductor project! 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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1kyfLrRYAiZZ_fWsf98SV1hYkMTOLgwqVDdTfV020wdiTPUVyeDfNX52bOE38NRodwetY0_JUBulJ1z3XOJVHVRj5v52wlPxqkR06J2bidSUaf6ZkpZyy3dbfCf3kGRsuaLVQn-YrBztYg6IJOH5_9DCEwLnmtw1Jqx6RKYcNeTQuYNCJUUPeh8-_lO8P2HFjZUQPOp1o5U4kI_0zeTEtMeFuBmt5quK2E_WgSvpMqhIMtgjAZ3Dm5WKomhDmHEADJ-tzc974XoB4kyUswhPLQptNIWYsG_pCCl9J2YLdNqMWGAJLyjgWGdLlM4KmF_d2/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.
* It is possible that the problems reported in this report are false positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.
* Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.
* If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:
https://bioconductor.org/help/mailing-list/<https://secure-web.cisco.com/13ShfWUilJ7HSUJJNxhvdff22zE5_XmjO_2QCpkqfTBSByH9dEez9DqMIFyK1_2iwGwalvz95hRGjr3HkgE2LhTtkN873R3RUb899FqzdozKq1jkWiUOXk0NyF4VsVoO44oIYwzGzr4gf5H_im36jyzQs0nrHsW4DJS_e-ret7bTQmLN-S62P4Pz73cGDbZWhcXyCQFwcJBG3xZnNbp_Cc6hooFH2W9C_Yk5YVErSOwXZ4cLJ-9rHK1R53MlwcVtyRIjCxXXB-YXLg2SfJoF7NsexkgaPagQPLB08iyb39E1bxRXA3MwpRvWdBmjEW1-b/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F>
(all package maintainers are requested to subscribe to this list)
For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:
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Thanks for contributing to the Bioconductor project!
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.
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