[Bioc-devel] REMP package commit and update

[Yinan Zheng]

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


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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