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 at gmail.com>
*Sent:* Tuesday, August 6, 2019 6:47:51 PM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Bioc-devel <bioc-devel at 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 at 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 at gmail.com>
*Sent:* Monday, August 5, 2019 12:17:29 PM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Bioc-devel <bioc-devel at 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 at 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 at git.bioconductor.org:packages/banocc (fetch)
origin git at 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 at git.bioconductor.org:packages/banocc (fetch)
*upstream* git at 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 at 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 at git.bioconductor.org:packages/banocc (fetch)
origin git at 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 at gmail.com>
*Sent:* Monday, August 5, 2019 10:48:30 AM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Bioc-devel <bioc-devel at 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 at git.bioconductor.org:packages/banocc (fetch)
origin git at 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 at 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 at gmail.com>
*Sent:* Sunday, August 4, 2019 4:43:15 PM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Bioc-devel <bioc-devel at 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 at 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 at 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 at gmail.com>
*Sent:* Thursday, August 1, 2019 2:57:21 PM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Bioc-devel <bioc-devel at 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 at 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 at 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 at 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