[Bioc-devel] Bioconductor Package Version

Fri Apr 23 15:00:30 CEST 2021

Hi AJ,

This issue has been resolved.  You should be able to push versions from 1.23.2 and onwards.

Going forward, please make sure to check your version numbers for both release and devel.

Check if your files have git merge conflicts.

Most importantly, if you have questions please ask either on the slack channel or on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> mailing list.

Best,

Nitesh

From: AJ Kinstlick <akinstlick using uchicago.edu>
Date: Thursday, April 22, 2021 at 6:37 PM
To: Nitesh Turaga <nturaga.bioc using gmail.com>
Cc: Kern, Lori <Lori.Shepherd using roswellpark.org>
Subject: Re: [Bioc-devel] Bioconductor Package Version
Hi Nitesh and Lori,
I wanted to check in and see if there was anything else I could do at this time to try and fix these version numbers. Will you guys be able to update it manually if nothing else works?
Thanks,
AJ

On Tue, Apr 20, 2021 at 2:39 PM Nitesh Turaga <nturaga.bioc using gmail.com<mailto:nturaga.bioc using gmail.com>> wrote:
Hi,

Thanks for looping me in.

I�ll take a look at this and keep you posted.

Best,

Nitesh

From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Date: Tuesday, April 20, 2021 at 3:36 PM
To: AJ Kinstlick <akinstlick using uchicago.edu<mailto:akinstlick using uchicago.edu>>, Nitesh Turaga <nturaga.bioc using gmail.com<mailto:nturaga.bioc using gmail.com>>
Subject: Re: [Bioc-devel] Bioconductor Package Version
Hey Nitesh,

I think we might have to force push a version up to straighten this out?  Can you please assist.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: AJ Kinstlick <akinstlick using uchicago.edu<mailto:akinstlick using uchicago.edu>>
Sent: Tuesday, April 20, 2021 3:34 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Subject: Re: [Bioc-devel] Bioconductor Package Version

Hi Lori,
I tried to push the package with version 1.23.1 and got the error "Illegal version bump from '1.18.0' to '1.23.1'.
Do you know if there's anything I can do?
Thanks,
Arjun

On Mon, Apr 19, 2021 at 2:03 PM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
At Bioconductor releases, the core team increases the version numbers of all packages.   It is important to remember to git pull upstream master  after each Bioconductor release before making any further changes to package and to resolve all DESCRIPTION file merge conflicts appropriately using the Bioconductor version number or higher.

At release we bumped the release 3.12 version of the package to 1.22.0 and devel version of the package to 1.23.0 which is reflected in the landing page and the built version of the package.

Somewhere along the way you had a merge conflict and changed the version back down to 1.18.0 in devel.  This is not supposed to be possible but managed to slip through our checks.

Version numbers should NEVER go down!

Please try and change the version number to 1.23.1 and try to push to the master branch again. If you continue to have issues, please reach back out.

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 using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of AJ Kinstlick <akinstlick using uchicago.edu<mailto:akinstlick using uchicago.edu>>
Sent: Monday, April 19, 2021 2:28 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Bioconductor Package Version

Hello,
I am trying to update the package seq2pathway.data, and I'm getting a
message that says "built version is LOWER than in internal repository".
Does anyone know how I can correct this error with my version numbers?

Trying to commit having directly bumped the version number fails.
It appears that the release version (
https://secure-web.cisco.com/1LH1a9lQCskb-SIBRlxp8f9spU0u2LNHud5_T6RYShbRqpMlBTwliMU78f7NlHz79tyzG2n6EWTNid7Lqy5fzQJGv81OhraorQ0DD-LsvscJaix2k19oDjQmvfi9bjcWp7nTl3QGFIfqsQbr0Ahk0xLjYmM6NtRJ1tXPa_Y0MbSE7XUBPCPVQShfnNYm16q0jiVuGjBXdO9iICW5t2TwrBXU4AYB2aaozpemovsNZpHsQ1ZhBWwJuI4H5galFMNzpVbmnrwRlEopQ8AcVtVGjJGIP_5selfIXdAYJtJEvu06MthoNbQ2xTI4yNS0MLbwCqiHh-W0Oc6k4E5ST0T8QRA/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fexperiment%2Fhtml%2Fseq2pathway.data.html<https://urldefense.com/v3/__https:/secure-web.cisco.com/1WUkdyaZv0BnyI_3kaNdttR3xK_jy3xnmg0kUb6CRtZespvTPlexJFvrk3QpYavvM-wVnAioZ0kJCS9PxFTXJHBN-SEwpVL-Y3OJA3uG4zFxbG6-FY2naW_fX_BuKFAck-AnRvYUcftprLvS3_frkXiKTRoj56p9Ui1WOeFoChRC4GQwBmOafhXZBcu3joijIjp44iY578_QiALw_ZYQ7KkNSqG2TpumPe7AVd7jtlOk29XfZqIaNTscU-Wd0xyBLYbY6ytuOr677PUGkmM9s0aiVroWO-IDvmGjwxDERaEqVp3jj_UlpPSiAoRQqZnyN/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1LH1a9lQCskb-SIBRlxp8f9spU0u2LNHud5_T6RYShbRqpMlBTwliMU78f7NlHz79tyzG2n6EWTNid7Lqy5fzQJGv81OhraorQ0DD-LsvscJaix2k19oDjQmvfi9bjcWp7nTl3QGFIfqsQbr0Ahk0xLjYmM6NtRJ1tXPa_Y0MbSE7XUBPCPVQShfnNYm16q0jiVuGjBXdO9iICW5t2TwrBXU4AYB2aaozpemovsNZpHsQ1ZhBWwJuI4H5galFMNzpVbmnrwRlEopQ8AcVtVGjJGIP_5selfIXdAYJtJEvu06MthoNbQ2xTI4yNS0MLbwCqiHh-W0Oc6k4E5ST0T8QRA*2Fhttps*2A3A*2A2F*2A2Fbioconductor.org*2A2Fpackages*2A2F3.13*2A2Fdata*2A2Fexperiment*2A2Fhtml*2A2Fseq2pathway.data.html__*3BJSUlJSUlJSUl*21*21BpyFHLRN4TMTrA*21tzz1bWVoSOmrEAxQLu7buEECrA3R1HuoHZE65xUOpI5VnR8_WqsaSnfpKKPFjyDUs_7v*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!BpyFHLRN4TMTrA!sTT02yYdQD87-HuGUOSMei2MfXF1PeXDleLVzZJgFCi8ec4hbUG1dElzGmH2n12t6-Gd$>)
is 1.23.0. However, the version that I'm working on (and that bioconductor
accepts when committing changes) is 1.18.0 (from
https://secure-web.cisco.com/1rIxCTN33O7HYcVU4fgfdpV6I4i9FmPYptspz4hPWUIyNVgawJrqd3T23nAxsOMNUCeGrNGgBxDnOIsgwXBPVXC44ds9TEmRKleV_r0yNPFkYdQpRMaMRP38sK1cRmG7WyYFX3udQykO6JAcmZxk-1md8g2bMBSklyLrLfm4lYFkVo0FcDZCtQFEkGL_74upqfBlrIJI1TXL2V-UipohLdHJOnHZ3QSMPBOZ5UHLIoW_Q2NA2C6M8U0qHmR7jHXyaH_t8EBIT35xPizQhkbmjnPf1nWWgpelGg0bXN9odWbxXMN37PwnxtFYXVJsC9qqXsBp6anVj0XAoTCR-KubbTQ/https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2F3.13%2Fdata-experiment-LATEST%2Fseq2pathway.data%2F<https://urldefense.com/v3/__https:/secure-web.cisco.com/1Ox9Bx-XIXwrrAxWEJTQMJg6HGQ0fPtT1vludrgwMZOVyy_eFUGp1SjzjA5bRbLryo1c_uQ6-ZtRPUyxrMBeC4yVpMux4dYlAUC8VNqLNea-jdb1ibauyguHgCJyu82pLSd8pYlwKDXiZNLbiZ79eCIKHUsGBC8aJyWBpWz_3PV0oR7KZGHuAP9Ac518sz60A63y6jUyyIydD2GVDy8B2cW0s__2BHHJPdMzgDbK9ooDiFAuAnqCLvifvuXGSA06jgrlxyqLp65PZBBMMLt7uPY_FkzBCumLWWVFJZncYvHP4NvvoMvRyZmmCHDa4igwy/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1rIxCTN33O7HYcVU4fgfdpV6I4i9FmPYptspz4hPWUIyNVgawJrqd3T23nAxsOMNUCeGrNGgBxDnOIsgwXBPVXC44ds9TEmRKleV_r0yNPFkYdQpRMaMRP38sK1cRmG7WyYFX3udQykO6JAcmZxk-1md8g2bMBSklyLrLfm4lYFkVo0FcDZCtQFEkGL_74upqfBlrIJI1TXL2V-UipohLdHJOnHZ3QSMPBOZ5UHLIoW_Q2NA2C6M8U0qHmR7jHXyaH_t8EBIT35xPizQhkbmjnPf1nWWgpelGg0bXN9odWbxXMN37PwnxtFYXVJsC9qqXsBp6anVj0XAoTCR-KubbTQ*2Fhttps*2A3A*2A2F*2A2Fwww.bioconductor.org*2A2FcheckResults*2A2F3.13*2A2Fdata-experiment-LATEST*2A2Fseq2pathway.data*2A2F__*3BJSUlJSUlJSU*21*21BpyFHLRN4TMTrA*21tzz1bWVoSOmrEAxQLu7buEECrA3R1HuoHZE65xUOpI5VnR8_WqsaSnfpKKPFjxw9weeF*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!BpyFHLRN4TMTrA!sTT02yYdQD87-HuGUOSMei2MfXF1PeXDleLVzZJgFCi8ec4hbUG1dElzGmH2n2qzAQ2y$>
).

Any help would be greatly appreciated.
Thank you,
Arjun Kinstlick

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Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://secure-web.cisco.com/1s8KFD9r1p8p5NsJBkNYQOhsQ98vGWbY6DnPTuke4g2XWrM7cPh3X_t4WeeIXf_qyKwQ6Gq-Uonn1IyszoxcGfZ6W9GrbQK-4qs0kFdnXEsfO4n-UABuQfINcYYXy-GOjKbNagE1FZ84Ne7ny9ArHRhfHyEkDZRDQER6BvO7lqzeBbkyzF7CfzLhji3Kypl8qx81Zd2bb2KwGO3nIuuBVsndFQBHoMgKfF8hvwAWK-KUOopd-Czfk7C5soniFQ3zE6I722-SeL_gcveKi5FU1iqsXwXfnExkXJgqUmk3UAY2NTLEI9WEtt1PMFEZURK3i-aiIs3lwUvpF9BWBvpVAAQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel<https://urldefense.com/v3/__https:/secure-web.cisco.com/1Zq_tSbidcnDAMz7snJXIw1lve7oNUJgKHXtuTOxz7e067EsL0I5VHk-hn-56qGrXWestGGXuyOj1ni0MmQzS8JL5Ach-gOHN6fZ6e4hk0_8mjcLy90jXkh_VGMPVYVzLS7RlPmwOkroRQS3G-1b1KpRAohqR0cFyWMUZXIVFV5FI2qIdBu58BC3TBuheNWNsqa-XFTzyRGA1JlZ1Rc9XpdT4VXrs0jODT1UCx28uGDBDCRU39tYA1Y2fiTDFFvrhDfH159X_QWyVH5HBonrrFnI0c-AkKD9S-r_HEygOLkksHuAR4Hbg5iOq01NPtojC/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1s8KFD9r1p8p5NsJBkNYQOhsQ98vGWbY6DnPTuke4g2XWrM7cPh3X_t4WeeIXf_qyKwQ6Gq-Uonn1IyszoxcGfZ6W9GrbQK-4qs0kFdnXEsfO4n-UABuQfINcYYXy-GOjKbNagE1FZ84Ne7ny9ArHRhfHyEkDZRDQER6BvO7lqzeBbkyzF7CfzLhji3Kypl8qx81Zd2bb2KwGO3nIuuBVsndFQBHoMgKfF8hvwAWK-KUOopd-Czfk7C5soniFQ3zE6I722-SeL_gcveKi5FU1iqsXwXfnExkXJgqUmk3UAY2NTLEI9WEtt1PMFEZURK3i-aiIs3lwUvpF9BWBvpVAAQ*2Fhttps*2A3A*2A2F*2A2Fstat.ethz.ch*2A2Fmailman*2A2Flistinfo*2A2Fbioc-devel__*3BJSUlJSUl*21*21BpyFHLRN4TMTrA*21tzz1bWVoSOmrEAxQLu7buEECrA3R1HuoHZE65xUOpI5VnR8_WqsaSnfpKKPFj_a0zTsN*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!BpyFHLRN4TMTrA!sTT02yYdQD87-HuGUOSMei2MfXF1PeXDleLVzZJgFCi8ec4hbUG1dElzGmH2n890VTGa$>

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