Dear all: I have been receiving messages that my Bionconductor package bigPint is producing errors on 'R CMD build' on malbec1. I believe I discovered the source of the error, fixed it, and pushed changes to my GitHub account ( github.com/lindsayrutter) on December 10, 2019. I continued to receive this error notification and was advised to ensure I had pushed the changes to Bioconductor. I pushed changes following these instructions ( http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am still receiving notifications that my package produces errors on 'R CMD build' on malbec1 ( https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html). However, it seems my package is no longer failing daily build reports for version 3.11 as of January 4, 2020 ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/). I am seeking advice on what a maintainer should try in this situation? Is it possible my changes were only recognized in version 3.11 but not version 3.10? Thank you for any advice you may have! Sincerely, L. Rutter
[Bioc-devel] R CMD build error for 3.10 (but not 3.11)
4 messages · L Rutter, Shepherd, Lori
2 days later
It looks like you only pushed changes to the master branch which is our devel branch (3.11). Please see the instructions for http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ where RELEASE_X_Y would be RELEASE_3_10 for pushing changes to the release 3.10 branch. Lori Shepherd 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 L Rutter <lindsayannerutter at gmail.com>
Sent: Saturday, February 1, 2020 4:18 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Sent: Saturday, February 1, 2020 4:18 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear all: I have been receiving messages that my Bionconductor package bigPint is producing errors on 'R CMD build' on malbec1. I believe I discovered the source of the error, fixed it, and pushed changes to my GitHub account ( github.com/lindsayrutter) on December 10, 2019. I continued to receive this error notification and was advised to ensure I had pushed the changes to Bioconductor. I pushed changes following these instructions ( http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am still receiving notifications that my package produces errors on 'R CMD build' on malbec1 ( https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html). However, it seems my package is no longer failing daily build reports for version 3.11 as of January 4, 2020 ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/). I am seeking advice on what a maintainer should try in this situation? Is it possible my changes were only recognized in version 3.11 but not version 3.10? Thank you for any advice you may have! Sincerely, L. Rutter [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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.
21 days later
Dear Lori: Thanks for the suggestions. I tried to follow the linked instructions on February 4 and February 9, but was unsuccessful both times (i.e. did not see the changes pushed to the release branch). I tried following the instructions again today. I notice that when I issue the command: git merge upstream/master I receive the message: merge: upstream/master - not something we can merge So, I clicked on the "Sync existing repositories" tab and checked that the instructions there were working. After adding the upstream branch as follows: git remote add upstream git at git.bioconductor.org:packages/bigPint.git When I then try to fetch all (git fetch --all), I receive the following error: Fetching origin Fetching upstream FATAL: R any packages/bigpint lrutter DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upstream I changed my GitHub userName about one year ago from "lrutter" to "lindsayrutter". By doing "git remote -v", I can see that my origin branches are correctly at "lindsayrutter", but I am unable to see about my upstream branches on git.bioconductor. This is my output from "git remote -v": origin https://github.com/lindsayrutter/bigPint (fetch) origin https://github.com/lindsayrutter/bigPint (push) upstream git at git.bioconductor.org:packages/bigpint.git (fetch) upstream git at git.bioconductor.org:packages/bigpint.git (push) Do you have any advice on how I can fix this issue with fetch upstream possibly expecting my older userName? Thank you for sharing advice. Sincerely, Lindsay 2020?2?3?(?) 21:54 Shepherd, Lori <Lori.Shepherd at roswellpark.org>:
It looks like you only pushed changes to the master branch which is our devel branch (3.11). Please see the instructions for http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ where RELEASE_X_Y would be RELEASE_3_10 for pushing changes to the release 3.10 branch. Lori Shepherd 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 L Rutter <lindsayannerutter at gmail.com> *Sent:* Saturday, February 1, 2020 4:18 AM *To:* bioc-devel at r-project.org <bioc-devel at r-project.org> *Subject:* [Bioc-devel] R CMD build error for 3.10 (but not 3.11) Dear all: I have been receiving messages that my Bionconductor package bigPint is producing errors on 'R CMD build' on malbec1. I believe I discovered the source of the error, fixed it, and pushed changes to my GitHub account ( github.com/lindsayrutter) on December 10, 2019. I continued to receive this error notification and was advised to ensure I had pushed the changes to Bioconductor. I pushed changes following these instructions ( http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am still receiving notifications that my package produces errors on 'R CMD build' on malbec1 ( https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html ). However, it seems my package is no longer failing daily build reports for version 3.11 as of January 4, 2020 ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/). I am seeking advice on what a maintainer should try in this situation? Is it possible my changes were only recognized in version 3.11 but not version 3.10? Thank you for any advice you may have! Sincerely, L. Rutter [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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.
Thank you for reaching out. Have you tried checking your keys and changing your name on the git.credentials app? https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: L Rutter <lindsayannerutter at gmail.com>
Sent: Tuesday, February 25, 2020 1:55 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Sent: Tuesday, February 25, 2020 1:55 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear Lori: Thanks for the suggestions. I tried to follow the linked instructions on February 4 and February 9, but was unsuccessful both times (i.e. did not see the changes pushed to the release branch). I tried following the instructions again today. I notice that when I issue the command: git merge upstream/master I receive the message: merge: upstream/master - not something we can merge So, I clicked on the "Sync existing repositories" tab and checked that the instructions there were working. After adding the upstream branch as follows: git remote add upstream git at git.bioconductor.org:packages/bigPint.git When I then try to fetch all (git fetch --all), I receive the following error: Fetching origin Fetching upstream FATAL: R any packages/bigpint lrutter DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upstream I changed my GitHub userName about one year ago from "lrutter" to "lindsayrutter". By doing "git remote -v", I can see that my origin branches are correctly at "lindsayrutter", but I am unable to see about my upstream branches on git.bioconductor. This is my output from "git remote -v": origin https://github.com/lindsayrutter/bigPint (fetch) origin https://github.com/lindsayrutter/bigPint (push) upstream git at git.bioconductor.org:packages/bigpint.git (fetch) upstream git at git.bioconductor.org:packages/bigpint.git (push) Do you have any advice on how I can fix this issue with fetch upstream possibly expecting my older userName? Thank you for sharing advice. Sincerely, Lindsay 2020年2月3日(月) 21:54 Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>>: It looks like you only pushed changes to the master branch which is our devel branch (3.11). Please see the instructions for http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ where RELEASE_X_Y would be RELEASE_3_10 for pushing changes to the release 3.10 branch. Lori Shepherd 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 L Rutter <lindsayannerutter at gmail.com<mailto:lindsayannerutter at gmail.com>> Sent: Saturday, February 1, 2020 4:18 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] R CMD build error for 3.10 (but not 3.11) Dear all: I have been receiving messages that my Bionconductor package bigPint is producing errors on 'R CMD build' on malbec1. I believe I discovered the source of the error, fixed it, and pushed changes to my GitHub account ( github.com/lindsayrutter<http://github.com/lindsayrutter>) on December 10, 2019. I continued to receive this error notification and was advised to ensure I had pushed the changes to Bioconductor. I pushed changes following these instructions ( http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am still receiving notifications that my package produces errors on 'R CMD build' on malbec1 ( https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html). However, it seems my package is no longer failing daily build reports for version 3.11 as of January 4, 2020 ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/). I am seeking advice on what a maintainer should try in this situation? Is it possible my changes were only recognized in version 3.11 but not version 3.10? Thank you for any advice you may have! Sincerely, L. Rutter [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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. 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.