The RSS error should be fixed.
On Sep 8, 2020, at 7:58 AM, Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>> wrote:
I RSS feed ERROR did not prevent the changes from being pushed to git.bioconductor.org<http://git.bioconductor.org/> . The changes should be reflected in either today's or tomorrow's build report. Please note: The package was failing in release and devel so don't forget to also push changes to RELEASE_3_11 branch (with appropriate release version number) Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Irene Zeng <i.zeng at auckland.ac.nz<mailto:i.zeng at auckland.ac.nz>>
Sent: Sunday, September 6, 2020 5:08 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>>; Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>>
Cc: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] fetch upstream of an existing package
Sent: Sunday, September 6, 2020 5:08 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>>; Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>>
Cc: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] fetch upstream of an existing package
Hello Lori, I have redone the merge and push, Now, it has pushed the changes, but I have the following messages: " $ git merge upstream/master Already up to date. OEM at OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (master) $ git push origin master Everything up-to-date OEM at OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (master) $ git push upstream master Enter passphrase for key '/c/Users/OEM/.ssh/id_rsa': Enumerating objects: 91, done. Counting objects: 100% (69/69), done. Delta compression using up to 8 threads Compressing objects: 100% (43/43), done. Writing objects: 100% (43/43), 6.42 KiB | 939.00 KiB/s, done. Total 43 (delta 32), reused 0 (delta 0), pack-reused 0 remote: fatal: this operation must be run in a work tree remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero exit status 128 remote: ERROR:root:local variable 'package_name' referenced before assignment remote: Note: failed to update RSS feed;git repository updated successfully. To git.bioconductor.org<http://git.bioconductor.org>:packages/sparsenetgls.git 2fef8fa..b8f64e4 master -> master " Do you know what the error messages tell us? Appreciate your guidance. Irene ________________________________ From: Irene Zeng Sent: Sunday, 6 September 2020 4:33 p.m. To: Shepherd, Lori; Turaga, Nitesh Cc: bioc-devel Subject: Re: [Bioc-devel] fetch upstream of an existing package I have done all the steps , after command "git merge upstream/master", it notified "Already up to date". But after I typed the command "git push upstream master", nothing happened, there was no further indication of whether the push was done. It looks like the changes were not pushed in the bioconductor repository. Thanks for your guidance, Irene ________________________________ From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>> Sent: Saturday, 5 September 2020 12:29 a.m. To: Irene Zeng; Turaga, Nitesh Cc: bioc-devel Subject: Re: [Bioc-devel] fetch upstream of an existing package This means that the auto merge could not resolve a file because there were changes in the upstream repository and in your current local branch. For best pratice a git merge upstream/master or git pull upstream master before making any changes locally will ensure you are working on the same version as upstream. Please edit the DESCRIPTION file to fix the merge conflict; they will be indicated with <<<<<<< HEAD some code ======= differing lines of code >>>>>>> Manually remove any lines you do not want to keep as well as the merge conflict indicators. For Bioconductor purposes looking at the current devel the version is 1.7.0 so make sure the version x.y.z has at least one z version bump (1.7.1). Once this is complete. Save your changes and do git add DESCRIPTION git commit You should then be able to continue with no ERRORs trying git merge upstream/master and should be able to proceed with git push upstream master. Cheers, 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 Irene Zeng <i.zeng at auckland.ac.nz<mailto:i.zeng at auckland.ac.nz>> Sent: Thursday, September 3, 2020 6:58 AM To: Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>> Cc: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> Subject: Re: [Bioc-devel] fetch upstream of an existing package Hello, Nitesh, The FAQ is very helpful. I have the remote access to the bioconductor repository now. The package is "sparsenetgls" and now can be cloned. I have checked all the changes in the updated version. I am going to commit changes in the bioconductor repository, but received the following error message: " $ git merge upstream/master Auto-merging DESCRIPTION CONFLICT (content): Merge conflict in DESCRIPTION Automatic merge failed; fix conflicts and then commit the result. " I have changed the description file, before the merge. I have also used fetch upstream, and then merge, I have received the following message: " $ git merge upstream/master error: Merging is not possible because you have unmerged files. hint: Fix them up in the work tree, and then use 'git add/rm <file>' hint: as appropriate to mark resolution and make a commit. fatal: Exiting because of an unresolved conflict. " Appreciated your guidance, with best wishes, Irene ________________________________ From: Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>> Sent: Thursday, 3 September 2020 1:17 a.m. To: Irene Zeng Cc: bioc-devel Subject: Fwd: [Bioc-devel] fetch upstream of an existing package Hi, Can you tell me which package you are talking about? Also, please take a look at the FAQ https://secure-web.cisco.com/1wHCYrF0I118lZ36UtYkkSKx1sjFZ6zqbQqSNpBSuCWxRVihubtXViEDhipMH68lVsPA-xv9ZzmHwebp48g7nqbBqBvNKjQ9zzZfz2X-OkMpSjNWoNVA6jRnqg0bDwZubOA1i0kHVVEw-zs9IaWDoOaGylQaLTyUmslOCo2ZyaOj8GtUwuNRwZArPaMV2yySt-Dr_39MEvQaKPjeJq8SXErkA1G8BPsit0oJlD2N9Q7v5bHHw_9wFZJd86nH48p1aJ_WhFPKwdLM79Ej2gX39Wvacpyyvm6rPasFGVE3hnKyzv-LStFl0ElC7fqXx1XcJ0eoq5M4b8SBJ7S5DSPv91w/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Ffaq%2F and see if there are any points there which address your concern. Specifically take a look at number 13 and 14. If you have any follow-up questions feel free to reach out. Best regards Nitesh On Aug 30, 2020, at 4:23 AM, Irene Zeng <i.zeng at auckland.ac.nz<mailto:i.zeng at auckland.ac.nz><mailto:i.zeng at auckland.ac.nz>> wrote: Dear Bioconductor core team, I am submitting changes to an existing package , I received the following error message when I used git to fetch upstream repository. I have received these message: " $ git fetch upstream git at git.bioconductor.org<mailto:git at git.bioconductor.org><mailto:git at git.bioconductor.org>: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. " I have added the publickey to the github account of the package, could you please advise? Irene ________________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org><mailto:bioc-devel-bounces at r-project.org>> on behalf of bioc-devel-request at r-project.org<mailto:bioc-devel-request at r-project.org><mailto:bioc-devel-request at r-project.org> <bioc-devel-request at r-project.org<mailto:bioc-devel-request at r-project.org><mailto:bioc-devel-request at r-project.org>> Sent: Tuesday, 25 August 2020 10:00 p.m. To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org> Subject: Bioc-devel Digest, Vol 197, Issue 21 Send Bioc-devel mailing list submissions to bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1pEetu3TkNnZOmWnv9FKlMC5oAf7aAbUtDzILVMvgGXC-NVyXedJRYTjOzMuB5OTizZHsdIGo7AhqepcMglQmY5QykI11sRZsqwN0VA8V-gyRx41QIhei_HJSv9ejT-c1pAoy2Z0omh78ltf7YK6EOmcmBvLwfRg55POF_zVeNxfgHWlv5O7HyVS9YHCbHOFJq-9X6jGhInYhz5sdOGG02xWKPBBCoPZnckmw-euUc8AQHtP_n2T8JdNikD1EMcU_yP_GvqjF7rFWz_0Q8vMFVxB-fO01SKq27tDU3uz1HrtJh7i0CV9JDk4Rg-zevl7jtgQ8nn9p3g59qeNb6dU1VA/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel or, via email, send a message with subject or body 'help' to bioc-devel-request at r-project.org<mailto:bioc-devel-request at r-project.org><mailto:bioc-devel-request at r-project.org> You can reach the person managing the list at bioc-devel-owner at r-project.org<mailto:bioc-devel-owner at r-project.org><mailto:bioc-devel-owner at r-project.org> When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioc-devel digest..." Today's Topics: 1. Re: About rcellminerData and rcellminerData new versions (Elloumi, Fathi (NIH/NCI) [C]) ---------------------------------------------------------------------- Message: 1 Date: Tue, 25 Aug 2020 00:01:37 +0000 From: "Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi at nih.gov<mailto:fathi.elloumi at nih.gov><mailto:fathi.elloumi at nih.gov>> To: =?utf-8?B?SGVydsOpIFBhZ8Oocw==?= <hpages at fredhutch.org<mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org>> Cc: "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org><mailto:Nitesh.Turaga at RoswellPark.org>>, "nitesh.turaga at gmail.com<mailto:nitesh.turaga at gmail.com><mailto:nitesh.turaga at gmail.com>" <nitesh.turaga at gmail.com<mailto:nitesh.turaga at gmail.com><mailto:nitesh.turaga at gmail.com>>, bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org>> Subject: Re: [Bioc-devel] About rcellminerData and rcellminerData new versions Message-ID: <F601D572-8465-4D58-B399-D944C8B76855 at nih.gov<mailto:F601D572-8465-4D58-B399-D944C8B76855 at nih.gov><mailto:F601D572-8465-4D58-B399-D944C8B76855 at nih.gov>> Content-Type: text/plain; charset="utf-8" Dear Herv?, Thank you very much for your clarification. I already pushed updates (more data) that will have impact on the output. I saw that you committed the April 27th version (2.10.0) for RELEASE_3_11. Looking at this link : https://secure-web.cisco.com/1cxOXcGjY8Xon6sy6Du8XC-Z04cU4qLi-vDuFylmb1eDAJjLxTaSLMmpBKEk6vN3esjCIqd9PtmqLZRGbeSvZei_NuVpysNBtRfRYJUCgOlmYWyBi7vJc0-8w4E9-rBetdT0vkaNe5wllpip0ODXycJ3S-EwOfoCKqdZ-B146kacTM-m2AO6zGrWExjOji4b1iw3wNGRyH_UrKDkLjJT_fIjMm_K7QaZzcoM6Vss9GmjIrYZc2otvn48Csyn-yCvDMjzbsdKBBrznj0GKObC24B78fck7dl7qTvIDL1UJpZ8nKL-Lx7OCU-0hlUbv47TOHQ3Im8HqTeftTmssC5XxUA/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fabandon-changes%2F , it seems that the Bioconductor team can reset a previous commit. Please let me know if this the right way to do it as described in the previous link. Please advise. Best, Fathi On 8/21/20, 5:45 PM, "Herv? Pag?s" <hpages at fredhutch.org<mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org>> wrote: Hi Fathi, The purpose of the "only bug fixes and documentation improvements in release" policy is **stability** of the current release (BioC 3.11). That is, we want to avoid disruption and to make analyses that use BioC 3.11 as reproducible as possible. This means that if the changes to the RELEASE_3_11 branch of the rcellminer and rcellminerData packages have the potential to break some of the scripts that your users are using for their analyses, or to change their output, then these changes should not be pushed to the RELEASE_3_11 branch. Note that we can only realistically aim at preserving things as stable as possible within the current release. Of course your software should be able to evolve over time. This is why important changes are allowed in devel (BioC 3.12). So the important question is: are the changes you pushed to BioC 3.11 going to preserve stability? You are in the best position to answer that question. We (Nitesh and myself) lack context to answer it. Maybe Daniel knows a little bit more about what kind of changes you made but unfortunately he's no longer part of the BioC core team. Bottom line is: If the changes don't preserve stability, please don't push them to the release branch. Please don't hesitate to ask on the bioc-devel mailing list if you have concerns or questions about this. Best, H. On 8/21/20 09:34, Elloumi, Fathi (NIH/NCI) [C] wrote: Dear Bioconductor team, As mentioned in my previous email (please see below), do you consider adding and cleaning data an enhancement should be only included in the develop branch and NOT in the current release (3_11) branch version but in the new release 3_12? I followed the instructions at https://secure-web.cisco.com/1i1Fj1PqXk5GA-p6NnS1S1ru0laY6C03kAxJYPtVeu-iYfKqr9EvoP6VrA3oEmNoXSNeqld9yFUGJQa0hF1tXLvVewTn9AQ7AVeKz35aGoIBSIB9ZMOgWgXwHJFQOQLT4B9gRUd1aDOLpIUAJJOXPSOSqVI9IDEwoEXzgoQAGfxrl33BK8n-IZFD_0qo1OvoOg6LzFLMMAT1ZM2bYLAYEuM0tjss-lQttzaPFG1--WzxD0nEH8KWUlNjIrRu2lza-MwkkodjN1ldgMM7fHG8htJq1kEWFHkR8Brc_sWyWrTUFVt7gZDyxcmgcAPwjBKLzmfpfUZtIfQHhuE__6TZcEw/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F <https://secure-web.cisco.com/1bu0fAauMRBlBzFIJ9PVK1ctP4mBuN1WSO2Qw9NBi6pc7ZJSmZ5zqh5S9a9K8jruAa1BHIeE25dc8ol1giFcyP-5nGPe7rf8zybfT1LuJXRgbc5VDg6FTDLmOj9jmYZUsWj21baSKUcD1Mp-0Dh_3GeiXAjp-utY8E7-Svcwap4FxrGsMAtlTATiYSXzgwFqln-srcHGrX0YGf6PCMH5f2WYOeqbN11J1bOjqX3mv3iRGQIMM767Pi12p8VX9_75BQLKp7DYR6nZiQxC6U71Mf7XTkJ-zIxselL0LjW6x1AQoyhxqprt6Ah9CqrCADTzz/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DARmhemKVIMghSoos_q1dvQqxgobSqzyAD0FygSN-ZKU%26s%3DTgJZrpJBaFZWeoPF8RdX5IiuL0buMRdvjYdIcWDdyNo%26e%3D> with instruction to update on both devel and release branches. Please advise. Best, Fathi *From: *"Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi at nih.gov<mailto:fathi.elloumi at nih.gov><mailto:fathi.elloumi at nih.gov>> *Date: *Friday, August 21, 2020 at 10:51 AM *To: *"Van Twisk, Daniel" <Daniel.VanTwisk at RoswellPark.org<mailto:Daniel.VanTwisk at RoswellPark.org><mailto:Daniel.VanTwisk at RoswellPark.org>> *Subject: *About rcellminerData and rcellminerData new versions Dear Daniel, This week I pushed new version (2.10.2) for both packages rcellminer and rcellminerData in the release_3_11 adding new drug data and cleaning some ?bad? experiments. Do you consider this against your policy here below. /From the Bioconductor paper in 2004/ /(//https://secure-web.cisco.com/13o4KCZVOAMdpJ1SkMUe01DlHHaeAa_CYazYr8xzX2_TMJapSR1mKmmXJvVyJ3ONwwdo62IZHVqhWHWhA3EUAEiqmnzIDOp8BoR13giEreX4V-cS5U-hik9MCEkrIIR0HqceEuy0mXT4UzSVgO6Kmv71UJvOeeOnzHH3PlaWzfJrBy0-zT-e8nxqmHh-tW86f1TW77VFaNLiYr3bY3yLz-1aUsPjzQc7Wem4Gz_LMTuMWMT6m72RcDUrLnvVdN-GanH7-Dfc9WOvAlllK-Sah34UKhLPE-MVg1QLABOMg4tDWm2rP2WH8J3TskIATcrcJRvf3MsiLRK5obJbIc30Deg/https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fgb-2004-5-10-r80%2F <https://secure-web.cisco.com/1gFbb6Q7hlrks_nCs2Rx7xfNGGoGCfYEjBoijdvfe5kVB5z2MCJljqc-k2_q-YJgu25vgvlxuMWpsnbgQCBDtJUByAgXbyDr1yxaa-e4jXD_9NAL_O36dWRW3_3_JCtdS_afoTz3FAGSBrAeIs61jAjKD-MInVhCew8YcAy6kF9FCyZS9Z5k2guEpd2yOhIfgq9QNeb4USw8EBwq47mQgEwBQX56L7pyhjgY5OFxoqnu3a10FXOK7vkLu2GEEOI6dfgOCqOBaPHBPVf_921psMxDD95x2uD_Fk4RS5k7fTcTxim_ETC8faz8J6L_sZvkg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__genomebiology.biomedcentral.com_articles_10.1186_gb-2D2004-2D5-2D10-2Dr80%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DARmhemKVIMghSoos_q1dvQqxgobSqzyAD0FygSN-ZKU%26s%3DYLZtYlTV7z-tuoZq2DBOY6jMZviyPBSyBTh1plvFEzI%26e%3D>/<https://secure-web.cisco.com/1gFbb6Q7hlrks_nCs2Rx7xfNGGoGCfYEjBoijdvfe5kVB5z2MCJljqc-k2_q-YJgu25vgvlxuMWpsnbgQCBDtJUByAgXbyDr1yxaa-e4jXD_9NAL_O36dWRW3_3_JCtdS_afoTz3FAGSBrAeIs61jAjKD-MInVhCew8YcAy6kF9FCyZS9Z5k2guEpd2yOhIfgq9QNeb4USw8EBwq47mQgEwBQX56L7pyhjgY5OFxoqnu3a10FXOK7vkLu2GEEOI6dfgOCqOBaPHBPVf_921psMxDD95x2uD_Fk4RS5k7fTcTxim_ETC8faz8J6L_sZvkg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__genomebiology.biomedcentral.com_articles_10.1186_gb-2D2004-2D5-2D10-2Dr80%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DARmhemKVIMghSoos_q1dvQqxgobSqzyAD0FygSN-ZKU%26s%3DYLZtYlTV7z-tuoZq2DBOY6jMZviyPBSyBTh1plvFEzI%26e%3D%3E/>):/ /The only changes allowed to be made on the release version are bug/ /fixes and documentation improvements. This ensures that users will not/ /encounter radical new behaviors in code obtained in the release/ /version. All other changes such as enhancements or design changes are/ /carried out on the development branch [34]./ Please let me know asap and if needed we will back to previous commit. Thanks, -- Fathi Fathi Elloumi, PhD Sr. Bioinformatics Software Engineer Contractor GDIT Inc Developmental Therapeutics Branch NIH/NCI/CCR Phone: 240-760-6601 -- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. 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