[Bioc-devel] REMP package commit and update

Wed Aug 23 12:54:59 CEST 2017

On 08/22/2017 08:10 PM, Yinan Zheng wrote:
> Thank you Martin. I tried again and here are the outputs:
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (master)
> $ git checkout RELEASE_3_5
> Branch RELEASE_3_5 set up to track remote branch RELEASE_3_5 from upstream.
> Switched to a new branch 'RELEASE_3_5'
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (RELEASE_3_5)
> $ git cherry-pick master
> error: could not apply 6eb6a33... Fix bugs
> hint: after resolving the conflicts, mark the corrected paths
> hint: with 'git add <paths>' or 'git rm <paths>'
> hint: and commit the result with 'git commit'
> 
> (Here I go back and revise the version number)
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (RELEASE_3_5|CHERRY-PICKING)
> $ git add DESCRIPTION
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (RELEASE_3_5|CHERRY-PICKING)
> $ git commit -m "update RELEASE_3_5 REMP_1.0.1"
> [RELEASE_3_5 5a444ed] update RELEASE_3_5 REMP_1.0.1
>   Date: Fri Aug 18 22:53:26 2017 -0500
>   26 files changed, 175 insertions(+), 134 deletions(-)
>   create mode 100644 inst/CITATION
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (RELEASE_3_5)
> $ git push upstream RELEASE_3_5
> Enter passphrase for key '/c/Users/yzk256/.ssh/id_rsa':
> Counting objects: 31, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (23/23), done.
> Writing objects: 100% (31/31), 5.03 KiB | 0 bytes/s, done.
> Total 31 (delta 26), reused 12 (delta 8)
> To git.bioconductor.org:packages/REMP.git
>     e6be793..5a444ed  RELEASE_3_5 -> RELEASE_3_5
> 
> yzk256 at FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (RELEASE_3_5)
> $ git push origin RELEASE_3_5
> Enter passphrase for key '/c/Users/yzk256/.ssh/id_rsa':
> Counting objects: 32, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (24/24), done.
> Writing objects: 100% (32/32), 5.29 KiB | 0 bytes/s, done.
> Total 32 (delta 26), reused 12 (delta 8)
> remote: Resolving deltas: 100% (26/26), completed with 26 local objects.
> To github.com:YinanZheng/REMP.git
>   * [new branch]      RELEASE_3_5 -> RELEASE_3_5

yes, so this commit succeed and now appears in the bioconductor git 
repository. You could validate this by cloning a new repository in a 
temporary location; we are exploring other ways of browsing the 
repositories.

Martin

> 
> 
> Best,
> Yinan
> 
> 
> -----Original Message-----
> From: Martin Morgan [mailto:martin.morgan at roswellpark.org]
> Sent: Tuesday, August 22, 2017 6:46 PM
> To: Yinan Zheng; bioc-devel at r-project.org
> Subject: Re: REMP package commit and update
> 
> On 08/22/2017 06:45 PM, Yinan Zheng wrote:
>> Hi Martin,
>>
>> I have moved my package "REMP" maintenance workflow to git source
>> control as instructed and I committed a few bug fixes to both devel
>> and release last week. Everything works well. Just wonder which site
>> and how long will I be able to see the changes take effect.
> 
> The build report, e.g., for 'devel' is at
> 
>     https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_&d=DwID-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=ZT-giYy2YxRWKeKQx_bIIwv14aQFK3ni9vrzQZX2lTI&m=CJ9_iL6ZFLH_fBC6VyK7Ed8Nk9UoB-jJ8h18LfiAxuo&s=5n8rmGdws2UNSJaCvMwt86eHDVV54uEGI6njp6OlOk0&e=
>   
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_REMP_malbec1-2Dbuildsrc.html&d=DwID-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=ZT-giYy2YxRWKeKQx_bIIwv14aQFK3ni9vrzQZX2lTI&m=CJ9_iL6ZFLH_fBC6VyK7Ed8Nk9UoB-jJ8h18LfiAxuo&s=y9120TjLRiFDhCHo28ULBaFwkLGhpt6ziIJYH3Z6aPI&e=
> 
> The 'Last Commit' reported in the header on that page is 6eb6a33
> 
> git log shows
> 
> REMP$ git log -n 1 --oneline
> 6eb6a33 Fix bugs
> 
> and the commit includes this version bump
> 
> REMP$ git show HEAD DESCRIPTION|grep Version
> -Version: 1.1.1
> +Version: 1.1.2
> 
> On the package 'landing page'
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_3.6_bioc_html_REMP.html&d=DwID-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=ZT-giYy2YxRWKeKQx_bIIwv14aQFK3ni9vrzQZX2lTI&m=CJ9_iL6ZFLH_fBC6VyK7Ed8Nk9UoB-jJ8h18LfiAxuo&s=BJJoYwv_VhtE4feunssDgAdHCet1CeMEzmRGQX6gnJs&e=
> 
> we have version 1.1.2 available, which is the version corresponding to the updated version -- everything looks good!
> 
> For release it seems like there are no commits since the branch
> 
> 
> REMP$ git checkout RELEASE_3_5
> REMP$ git log --oneline -n 3
> e6be793 Creating branch for BioC 3.5 release
> 12e9632 bump x.y.z versions to even y prior to creation of 3_5 branch
> 5377642 0.99.25
> 
> so it looks like your release push did not succeed? Maybe you can try again and provide the output of your commands
> 
> Martin
> 
> 
>>
>> Thanks.
>>
>> Yinan Zheng
>>
>> Lead Bioinformatics/Statistical Analyst, Population Epigenetics Lab
>>
>> Cancer Epidemiology and Prevention
>>
>> Department of Preventive Medicine
>>
>> Northwestern University Feinberg School of Medicine
>>
>> 312-503-5337 <tel:312-503-5337>
>>
>> y-zheng at northwestern.edu <mailto:y-zheng at northwestern.edu>
>>
> 
> 
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