[Bioc-devel] banocc: Bioconductor BUILD error

Wed Aug 7 05:41:50 CEST 2019

Lori,
Thanks for all your help!
George

On Tue, Aug 6, 2019 at 5:22 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> That should be good to push to the release branch. I will check tomorrow
> and keep and eye on the build report but on quick glance it looks correct.
> Thank you for all your effort on this.
> Cheers
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------------------------------
> *From:* George Weingart <george.weingart using gmail.com>
> *Sent:* Tuesday, August 6, 2019 6:47:51 PM
>
> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> *Cc:* Bioc-devel <bioc-devel using r-project.org>
> *Subject:* Re: banocc: Bioconductor BUILD error
>
> Hi Lori,
>
> I followed all the instructions in
> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/.
> See log below.
> Is there anything that I need to do at this point ?
>
> Thanks so much for all your help !
>
> George Weingart PhD
> Huttenhower Lab
> Harvard School of Public Health
>
> *Log:*
>
> Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION
>
> Tanias-MacBook-Air:banocc georgeweingart$ git status
>
> On branch RELEASE_3_9
>
> Your branch is ahead of 'upstream/RELEASE_3_9' by 4 commits.
>
>   (use "git push" to publish your local commits)
>
> Changes not staged for commit:
>
>   (use "git add <file>..." to update what will be committed)
>
>   (use "git checkout -- <file>..." to discard changes in working directory)
>
> modified:   DESCRIPTION
>
> no changes added to commit (use "git add" and/or "git commit -a")
>
> Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION
>
> Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Updated version
> number"
>
> [RELEASE_3_9 3bf4a1d] Updated version number
>
>  1 file changed, 1 insertion(+), 1 deletion(-)
>
> Tanias-MacBook-Air:banocc georgeweingart$ git push upstream RELEASE_3_9
>
> Enumerating objects: 8, done.
>
> Counting objects: 100% (8/8), done.
>
> Delta compression using up to 4 threads
>
> Compressing objects: 100% (6/6), done.
>
> Writing objects: 100% (6/6), 573 bytes | 573.00 KiB/s, done.
>
> Total 6 (delta 4), reused 0 (delta 0)
>
> To git.bioconductor.org:packages/banocc
>
>    e689ef5..3bf4a1d  RELEASE_3_9 -> RELEASE_3_9
>
>
> On Mon, Aug 5, 2019 at 9:34 AM Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
>> Hi George,
>>
>>
>> No problem at all.  We are glad to help and glad you are being so
>> cautious.
>>
>>
>> I am able to see the successful commit/changes on devel (master branch).
>> So that has been successful.
>>
>>
>> You would need to make similar changes to the RELEASE_3_9 branch as your
>> package was failing in both release and devel
>>
>>
>> release build report:
>>
>> http://bioconductor.org/checkResults/release/bioc-LATEST/banocc/
>>
>>
>> So yes the
>> (Optional) Merge changes to the current release branch
>> does apply.
>>
>> A note about these commands:
>>
>> git merge master
>>
>> will merge all the files from the current devel branch into the release
>> branch.  Sometime this is okay and recommended but sometimes this is not
>> what you want (if you has been testing features that are in the devel
>> branch but need to correct a bug on release).  Sometimes it's better to
>> checkout the release branch:
>>
>> git checkout -b <RELEASE_X_Y> upstream/<RELEASE_X_Y>
>>
>> git pull
>>
>>
>> but then individually modify and commit changes like you did for the
>> other branch.
>>
>>
>>
>> However, In this case you should be okay with a merge  -
>>
>>
>> The current release branch is RELEASE_3_9  (instead of RELEASE_X_Y in the
>> instructions)
>>
>>
>> Also note the version in the DESCRIPTION file for the RELEASE_3_9 branch
>> will need to be changed.  The current version is 1.8.0 so this should be
>> changed to 1.8.1  and committed before doing
>>
>>
>> git push upstream RELEASE_3_9
>>
>>
>>
>> Hopefully this all makes sense.  If something seems unclear don't
>> hesistate to ask.
>>
>>
>> Cheers,
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* George Weingart <george.weingart using gmail.com>
>> *Sent:* Monday, August 5, 2019 12:17:29 PM
>> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Cc:* Bioc-devel <bioc-devel using r-project.org>
>> *Subject:* Re: banocc: Bioconductor BUILD error
>>
>>
>> Hi Lori,
>>
>> I followed your instructions and went as far as “git push upstream master”
>>
>> Do I need to do the “(Optional) Merge changes to the current release
>> branch” ?
>>
>> As I mentioned, I am being extra careful so I do not damage the
>> repository.
>>
>> Thanks so much for your  help !!
>>
>> George
>>
>> Here is the log:
>>
>>
>> Tanias-MacBook-Air:Harvard georgeweingart$ git clone
>> git using git.bioconductor.org:packages/banocc
>>
>> Cloning into 'banocc'...
>>
>> remote: Enumerating objects: 142, done.
>>
>> remote: Counting objects: 100% (142/142), done.
>>
>> remote: Compressing objects: 100% (138/138), done.
>>
>> remote: Total 142 (delta 47), reused 0 (delta 0)
>>
>> Receiving objects: 100% (142/142), 25.33 MiB | 880.00 KiB/s, done.
>>
>> Resolving deltas: 100% (47/47), done.
>>
>> Tanias-MacBook-Air:Harvard georgeweingart$ cd banocc
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git remote -v
>>
>> origin git using git.bioconductor.org:packages/banocc (fetch)
>>
>> origin git using git.bioconductor.org:packages/banocc (push)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git remote rename origin
>> upstream
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git remote -v
>>
>> *upstream* git using git.bioconductor.org:packages/banocc (fetch)
>>
>> *upstream* git using git.bioconductor.org:packages/banocc (push)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ cd vignettes/
>>
>> Tanias-MacBook-Air:vignettes georgeweingart$ vim banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git status
>>
>> On branch master
>>
>> Your branch is up to date with 'upstream/master'.
>>
>> Changes not staged for commit:
>>
>>   (use "git add <file>..." to update what will be committed)
>>
>>   (use "git checkout -- <file>..." to discard changes in working
>> directory)
>>
>> modified:   DESCRIPTION
>>
>> modified:   vignettes/banocc-vignette.Rmd
>>
>> no changes added to commit (use "git add" and/or "git commit -a")
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add
>> vignettes/banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Modified date
>> in the DESCRIPTION and removed reference to c+11 in vignette"
>>
>> [master e59c70c] Modified date in the DESCRIPTION and removed reference
>> to c+11 in vignette
>>
>>  2 files changed, 1 insertion(+), 2 deletions(-)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$  git checkout master
>>
>> Already on 'master'
>>
>> Your branch is ahead of 'upstream/master' by 1 commit.
>>
>>   (use "git push" to publish your local commits)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git push upstream master
>>
>> Enumerating objects: 9, done.
>>
>> Counting objects: 100% (9/9), done.
>>
>> Delta compression using up to 4 threads
>>
>> Compressing objects: 100% (5/5), done.
>>
>> Writing objects: 100% (5/5), 472 bytes | 472.00 KiB/s, done.
>>
>> Total 5 (delta 4), reused 0 (delta 0)
>>
>> To git.bioconductor.org:packages/banocc
>>
>>    d145287..e59c70c  master -> master
>>
>>
>> On Mon, Aug 5, 2019 at 7:56 AM Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>
>> So you only have a Bioconductor git repository,
>>
>> not your own github repository to also keep track of changes?
>>
>>
>> Then these instructions are correct:
>>
>>  http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
>>
>> We normal recommend changing the name of the remote from origin to
>> upstream so that it is consistent with all the help documentation (Step #4
>> above) we have written.
>>
>>
>> If you do not want to rename  then the following will push to the git
>> bioconductor repository,
>>
>> git push origin RELEASE_3_9
>>
>>
>> The syntax of a git command like git push or git pull  can be broken down
>> to
>>
>> git push  <name of remote>  <name of branch>
>>
>>
>> so git push origin RELEASE_3_9
>>
>>
>> based on git remote -v
>>
>> your origin remote points to the git.bioconductor.org location
>>
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git remote -v
>> origin git using git.bioconductor.org:packages/banocc (fetch)
>> origin git using git.bioconductor.org:packages/banocc (push)
>>
>> So git push origin RELEASE_3_9
>>
>> will push to the bioconductor git repository (your origin remote)  and to
>> the RELEASE_3_9 branch.
>>
>>
>>
>> Hope this helps
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* George Weingart <george.weingart using gmail.com>
>> *Sent:* Monday, August 5, 2019 10:48:30 AM
>> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Cc:* Bioc-devel <bioc-devel using r-project.org>
>> *Subject:* Re: banocc: Bioconductor BUILD error
>>
>>  Hi Lori,
>> Here is the display you wanted to see.
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ *git remote -v*
>>
>> origin git using git.bioconductor.org:packages/banocc (fetch)
>>
>> origin git using git.bioconductor.org:packages/banocc (push)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$
>>
>>
>> So what should the next step be?
>>
>>
>> I don't want to 'try'  things so I do not cause damage to the repository .
>>
>>
>> Thanks!
>>
>> George Weingart
>>
>>
>> Thanks!
>>
>>
>>
>> On Mon, Aug 5, 2019 at 5:01 AM Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>
>> Can you please display the results from
>>
>>
>> git remote -v
>>
>>
>> It looks like you may have not setup the remote to point to the
>> Biocondutor repository.
>>
>>
>> # 2 from here:
>>
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>
>>
>>
>> The code below looks like it is pulling and comparing to origin  which is
>> normally your own github repository not the Bioconductor git repository.
>>
>>
>> If you did not have a github repository and were only linking to
>> Bioconductor (not normally the case but possible) See #4
>> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/.
>>
>>
>>
>> Again most likely you will want this not the above:
>>
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>
>>
>> Please also consider glancing at more of the following help steps
>>
>> http://bioconductor.org/developers/how-to/git/
>>
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* George Weingart <george.weingart using gmail.com>
>> *Sent:* Sunday, August 4, 2019 4:43:15 PM
>> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Cc:* Bioc-devel <bioc-devel using r-project.org>
>> *Subject:* Re: banocc: Bioconductor BUILD error
>>
>> Hi Lori and Bioc-Devel,
>>
>> I followed Lori's instructions but the push is failing - I must be doing
>> something wrong.
>> Here is the log:
>>
>> Can you tell me how to do it right ?
>>
>> Thanks!
>> George Weingart PhD
>> Huttenhower Lab
>> Harvard School of Public Health
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git checkout RELEASE_3_9
>>
>> Branch 'RELEASE_3_9' set up to track remote branch 'RELEASE_3_9' from
>> 'origin'.
>>
>> Switched to a new branch 'RELEASE_3_9'
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git pull
>>
>> Already up to date.
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION
>>
>> Tanias-MacBook-Air:vignettes georgeweingart$ vim banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:vignettes georgeweingart$ git status
>>
>> On branch RELEASE_3_9
>>
>> Your branch is up to date with 'origin/RELEASE_3_9'.
>>
>> Changes not staged for commit:
>>
>>   (use "git add <file>..." to update what will be committed)
>>
>>   (use "git checkout -- <file>..." to discard changes in working
>> directory)
>>
>> modified:   ../DESCRIPTION
>>
>> modified:   banocc-vignette.Rmd
>>
>> no changes added to commit (use "git add" and/or "git commit -a")
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add
>> vignettes/banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git status
>>
>> On branch RELEASE_3_9
>>
>> Your branch is up to date with 'origin/RELEASE_3_9'.
>>
>> Changes to be committed:
>>
>>   (use "git reset HEAD <file>..." to unstage)
>>
>> modified:   DESCRIPTION
>>
>> modified:   vignettes/banocc-vignette.Rmd
>>
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Updated:
>> Release to 1.8.1 and removed C+11 references that were causing BUILD to
>> fail"
>>
>> [RELEASE_3_9 26bd0f7] Updated: Release to 1.8.1 and removed C+11
>> references that were causing BUILD to fail
>>
>>  2 files changed, 2 insertions(+), 4 deletions(-)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git push upstream RELEASE_3_9
>>
>> fatal: 'upstream' does not appear to be a git repository
>>
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights
>>
>> and the repository exists.
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git push origin/RELEASE_3_9
>>
>> fatal: 'origin/RELEASE_3_9' does not appear to be a git repository
>>
>> fatal: Could not read from remote repository.
>>
>>
>> On Fri, Aug 2, 2019 at 4:52 AM Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>
>> Hello,
>>
>>
>> The package was failing in release and devel.  There are two separate
>> branches in Bioconductor.
>>
>>
>> The master branch of a package is always the devel branch of
>> Bioconductor where you pushed "1.9.1".  We do see this clean report.
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/banocc/
>>
>>
>>
>> You will also have to make and push changes to the RELEASE_3_9  branch on
>> bioconductor and bump the version to "1.8.1".
>>
>> http://bioconductor.org/checkResults/release/bioc-LATEST/banocc/
>>
>>
>>
>> This help page references fixes on a RELEASE branch:
>>
>>
>> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>>
>> Summary:
>>
>>
>> git fetch --all
>>
>> git checkout -b RELEASE_3_9  upstream/RELEASE_3_9
>> # or if you have already done this once
>> # git checkout RELEASE_3_9
>>
>> git pull
>>
>> # make necessary changes to code
>> # add and commit with a valid version bump (1.8.1)
>> # git add / git commit
>>
>> git push upstream RELEASE_3_9
>>
>>
>> Hope this helps!  If you have further git issues for pushing to release I
>> suggest checking out the help pages and then asking on the
>> bioc-devel using r-project.org mailing list so that others may assist as well.
>>
>>
>> Cheers,
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* George Weingart <george.weingart using gmail.com>
>> *Sent:* Thursday, August 1, 2019 2:57:21 PM
>> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Cc:* Bioc-devel <bioc-devel using r-project.org>
>> *Subject:* Re: banocc: Bioconductor BUILD error
>>
>> Hi Lori,
>>
>> I pushed about two weeks ago the changes that result in a good Build and
>> Check at version 1.9.1 (of Banocc)  but I am still getting errors
>> pertaining to Build at release 1.8.0.
>>
>> Did I do something wrong ?  Perhaps I did not push correctly ?
>>
>> Can I trouble you to look at it and let me know?
>>
>> Thanks and best regards,
>> George Weingart PhD
>> Huttenhower Lab
>> Harvard School of Public Health
>>
>> On Mon, Jul 15, 2019 at 5:57 PM George Weingart <
>> george.weingart using gmail.com> wrote:
>>
>> Hello Lori,
>>
>> Done !
>>
>> I removed the two references to c++11 from the package,  ran a BUILD and
>> a CHECK and they were clean.
>> Pushed the changes.
>>
>> Below,  the log of the push.
>>
>> Let me know what you find in the BiocCheck space pertaining the Sweave
>> error.
>>
>> Thank you !
>> Best regards,
>> George Weingart PhD
>> Huttenhower Lab
>> Harvard School of Public Health
>>
>> LOG OF PUSH
>>
>> Tanias-MacBook-Air:Harvard georgeweingart$ cd banocc
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git status
>>
>> On branch master
>>
>> Your branch is up to date with 'origin/master'.
>>
>> Changes not staged for commit:
>>
>>   (use "git add <file>..." to update what will be committed)
>>
>>   (use "git checkout -- <file>..." to discard changes in working
>> directory)
>>
>> modified:   DESCRIPTION
>>
>> modified:   vignettes/banocc-vignette.Rmd
>>
>> no changes added to commit (use "git add" and/or "git commit -a")
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git add
>> vignettes/banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git status
>>
>> On branch master
>>
>> Your branch is up to date with 'origin/master'.
>>
>> Changes to be committed:
>>
>>   (use "git reset HEAD <file>..." to unstage)
>>
>> modified:   DESCRIPTION
>>
>> modified:   vignettes/banocc-vignette.Rmd
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Removed c++11
>> references that are making BUILD fail in R3.6.0"
>>
>> [master d145287] Removed c++11 references that are making BUILD fail in
>> R3.6.0
>>
>>  2 files changed, 2 insertions(+), 4 deletions(-)
>>
>> Tanias-MacBook-Air:banocc georgeweingart$ git push
>>
>> Enumerating objects: 9, done.
>>
>> Counting objects: 100% (9/9), done.
>>
>> Delta compression using up to 4 threads
>>
>> Compressing objects: 100% (5/5), done.
>>
>> Writing objects: 100% (5/5), 481 bytes | 481.00 KiB/s, done.
>>
>> Total 5 (delta 4), reused 0 (delta 0)
>>
>> To git.bioconductor.org:packages/banocc
>>
>>    5aefed9..d145287  master -> master
>>
>>
>> On Mon, Jul 15, 2019 at 11:35 AM George Weingart <
>> george.weingart using gmail.com> wrote:
>>
>> Thanks Lori!
>>
>> Will do.
>>
>> Let me know about BiocCheck.
>>
>> Thanks!
>> George Weingart
>>
>> On Mon, Jul 15, 2019 at 10:26 AM Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>
>> I can look into the BiocCheck ERROR for future development. It would be
>> good to figure out why this is happening.  But in the meantime,  if your
>> solution passes R CMD build and R CMD check please continue with pushing to
>> the git.bioconductor.org server  as BiocCheck is not run on the nightly
>> builds.
>>
>>
>> Cheers,
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>>

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