From: Xiaowen Chen <Xiaowen.Chen at jax.org>
Sent: Saturday, October 17, 2020 2:40 PM
To: Martin Morgan <mtmorgan.bioc at gmail.com>; Kern, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update
Yes, the check report is the one I lately push,
But the epihet on the website" bioconductor.org/packages/devel/bioc/html/epihet.html " is not the one latest through check the vignettes.
So now I updated the version in DESCRIPTION to 1.5.3, and push again and hope I can see the latest version on the website " bioconductor.org/packages/devel/bioc/html/epihet.html "
Thank you.
Best,
Xiaowen
On 10/17/20, 10:26 AM, "Martin Morgan" <mtmorgan.bioc at gmail.com> wrote:
Packages are built nightly, so you must usually wait ~24 - 48 hours for your commits to be reflected in the build report.
Sometimes issues prevent the build report from being processed, so on the build overview page such as
http://secure-web.cisco.com/1Ktwhc-1fOD537-R0w6DZa7xx108gqW4GXONiL_FjB0P1DtGxH_Ts1H15R1oCNf20fTFBPForRU_uweA01_tMeLAiwRSKQ0Q_xCj2Z8jLcpBwyrTHakwW74B7Ej_esnheP6s97mLq0G8HufjxWCAMyPXrqxWK_2H0JRC050653eLkp30aJip-dZMb20BmCg6xzhw1Mqd_Pu4vxReOYEhWo_pazA4USiF82BebUOt0QWntEYAreDEZS0vPfkJgw6aINuP68uLLmrlKKymPFPGzZyK5M0xoICUDwMpvAJBzlGs8GH5WWpS6wQFicGIs3S9K/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2F
compare
- 'This page generated on...'
- 'Approx snapshot date...'
and on individual package pages such as
http://secure-web.cisco.com/1zdf9ads4VET4y3GW4X3aCfi4cSdGfENmczEK6FJ9MQ-WEKuGct0QO0SntkvNKCDJZ37-wOYUmiXrFyshe1xTL5sQgKZLac_kzk0nrloIqi13Pc10llxMUAxmJ_-ND5PH6hH_TxA9lo4zvnrATrDRn-cFkx-n_mqGlOeOTrj9xBy7o-KJcXDInohJncsDSiEJYNz4sfxfTCnL-eSaoLBf1RhXMP8_nUU8dEbmTm_CFielxiaHfiyL7icRTqu0la8VqPm-a13wu_5O6JShbyKShYvUTZ4vSL14pj0zExjvkRHMMqcjMOpGZbRRGlqt1Rge/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fepihet%2F
look for
- 'Snapshot date...'
- 'Last commit...'
If your last commit (`git log --oneline`) was after the snapshot date, then changes you made will not be reflected in the build report.
Because of the delay in the nightly builds, it makes sense to do your best to ensure that commits are correct, ensuring that your R and Bioconductor packages are current for the version that you are committing to, and running
R CMD build <pgk>
R CMD check <pkg_....tar.gz>
locally before pushing changes.
Martin
On 10/16/20, 5:08 PM, "Bioc-devel on behalf of Xiaowen Chen" <bioc-devel-bounces at r-project.org on behalf of Xiaowen.Chen at jax.org> wrote:
Hi Kern,
I checked the epihet on the website ?bioconductor.org/packages/devel/bioc/html/epihet.html?.
I saw its version is 1.5.2
Unfortunately, it is not the one I push this morning. It is not the latest one.
Could you help me check what?s wrong here? I am so sorry about that.
Best,
Xiaowen
From: "Kern, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Friday, October 16, 2020 at 9:54 AM
To: Xiaowen Chen <Xiaowen.Chen at jax.org>, "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: [EXTERNAL]Re: A question about r package update
We apologize. It was announced on the Bioconductor slack but we forgot to post on the bioc-devel mailing list. There was an issue with the builders and there was no report generated yesterday Thursday October 15. The issue should be resolved and we expect a build report today.
I do see 1.5.2 in our git repository so it should be reflected in the report today.
We apologize for the confusion and the inconvenience
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 at r-project.org> on behalf of Xiaowen Chen <Xiaowen.Chen at jax.org>
Sent: Friday, October 16, 2020 9:49 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] A question about r package update
Hi bioc-devel,
I am sorry for email you so often, this morning I checked the check report website, it did not change.
And I noticed that the data is ?This page was generated on 2020-10-14 11:07:41 -0400 (Wed, 14 Oct 2020).?
Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 1.5.1 shown in the website.
Even it is not the one I pushed, now it have been two days.
So this morning I push epihet again. The command is as following
(base) [chenx at helix epihet]$ git remote add upstream git at git.bioconductor.org:packages/epihet.git
(base) [chenx at helix epihet]$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
From git.bioconductor.org:packages/epihet
* [new branch] RELEASE_3_10 -> upstream/RELEASE_3_10
* [new branch] RELEASE_3_11 -> upstream/RELEASE_3_11
* [new branch] RELEASE_3_9 -> upstream/RELEASE_3_9
* [new branch] master -> upstream/master
(base) [chenx at helix epihet]$ git checkout master
Already on 'master'
(base) [chenx at helix epihet]$ git merge origin/master
Already up-to-date.
(base) [chenx at helix epihet]$ git merge upstream/master
Already up-to-date.
(base) [chenx at helix epihet]$ git push upstream master
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
Everything up-to-date
(base) [chenx at helix epihet]$ git push origin master
Everything up-to-date
Previously, when I typed ?git merge upstream/master?, it returned something like this
Merge made by recursive.
DESCRIPTION | 2 +-
NEWS | 7 +++++--
2 files changed, 6 insertions(+), 3 deletions(-)
mode change 100755 => 100644 DESCRIPTION
So I am curious whether epihet1.5.2 successfully push to upstream?
Could you help me to check? Since tomorrow is weekend.
Thank you pretty much.
Best,
Xiaowen
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