[Bioc-devel] Trigger a new build after version bump
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Dec 20 23:20:39 CET 2019
I think this is because of build failures of other packages on the Windows builder, as mentioned by Lori
https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015962.html
For instance, your package can’t find SummarizedExperiment, because when the build system tried to install SummarizedExperiment it failed
http://bioconductor.org/checkResults/release/bioc-LATEST/SummarizedExperiment/tokay1-install.html
… because DelayedArray failed
http://bioconductor.org/checkResults/release/bioc-LATEST/DelayedArray/tokay1-install.html
… because BiocParallel failed
http://bioconductor.org/checkResults/release/bioc-LATEST/BiocParallel/tokay1-install.html
… because the CRAN package ‘snow’ failed to install, for reasons that are still under investigation.
There is nothing for you to do until this has been fixed on our end.
Martin
From: Ahmed Metwally <ametwall using stanford.edu>
Date: Friday, December 20, 2019 at 5:08 PM
To: Martin Morgan <mtmorgan.bioc using gmail.com>, "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Cc: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Trigger a new build after version bump
Thank you, Martin!
It worked exactly as you mentioned. Now the package has been built successfully, except for windows on the release branch. Here is the error: http://bioconductor.org/checkResults/release/bioc-LATEST/OmicsLonDA/tokay1-buildsrc.html
* installing the package to build vignettes
-----------------------------------
ERROR: dependencies 'SummarizedExperiment', 'BiocParallel' are not available for package 'OmicsLonDA'
* removing 'C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpULajPf/Rinst420c6eb71a2e/OmicsLonDA'
I have 'SummarizedExperiment' and 'BiocParallel' in the import section of the DESCRIPTION file:
https://github.com/aametwally/OmicsLonDA/blob/master/DESCRIPTION
Any help?
________________________________
From: Martin Morgan <mtmorgan.bioc using gmail.com>
Sent: Thursday, December 19, 2019 12:19 PM
To: Ahmed Metwally <ametwall using stanford.edu>; Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Trigger a new build after version bump
It seems like in your vignette you are trying to install your own package. But if you needed to install the package, then the vignette wouldn't be available to install it from... ;) In this code chunk
```{r results='hide',message=FALSE,warning=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager", repos = "http://cran.us.r-project.org")
BiocManager::install("OmicsLonDA")
```
Change the options to
```{r, eval = FALSE}
Martin
On 12/19/19, 2:22 PM, "Bioc-devel on behalf of Ahmed Metwally" <bioc-devel-bounces using r-project.org on behalf of ametwall using stanford.edu> wrote:
Hi,
The built is has been done on the updates I pushed. Here you see that the release version has been bumped to 1.2.1 instead of 1.2.0 and dev version has been bumped to 1.3.3 instead of 1.3.0.
However, I still see the same error as before. Here is the OS built results for the release branch: http://bioconductor.org/checkResults/release/bioc-LATEST/OmicsLonDA/merida1-buildsrc.html
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmicsLonDA
###
##############################################################################
##############################################################################
* checking for file �OmicsLonDA/DESCRIPTION� ... OK
* preparing �OmicsLonDA�:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building �OmicsLonDA.Rmd� using rmarkdown
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'OmicsLonDA'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/OmicsLonDA_1.2.0.tgz'
Content type 'application/x-gzip' length 5219591 bytes (5.0 MB)
In the above snippet, it says "trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/OmicsLonDA_1.2.0.tgz'
"
v1.2.0 is the old version. The new version is 1.2.1. Should I update anything to make sure BioC checks the new version "1.2.1"?
Thanks,
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ahmed Metwally <ametwall using stanford.edu>
Sent: Tuesday, December 17, 2019 4:58 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Trigger a new build after version bump
Great! Thank you, Lori
Ahmed A. Metwally
Sent from iPhone
On Dec 17, 2019, at 4:21 AM, Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>> wrote:
Jakob is correct. To expand a bit more:
The results will not be present on today's build report but should be there on tomorrows. We do a git pull around 4:45 PM EST for the daily builds. If commits are made after that (which it seems like in this case) it would be on the following days.
For What Its worth I do see your changes on git.bioconductor.org<http://git.bioconductor.org> so you were able to push them correctly.
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 using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Ahmed Metwally <ametwall using stanford.edu<mailto:ametwall using stanford.edu>>
Sent: Tuesday, December 17, 2019 2:49 AM
To: Jakob Theorell <jakob.theorell using ndcn.ox.ac.uk<mailto:jakob.theorell using ndcn.ox.ac.uk>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Trigger a new build after version bump
Hi Jakob,
Thanks for your explanation. I was looking for any statement about how long should I wait but couldn't find any. I pushed the updates around 6 hours ago. I'll wait for 24-48h as you suggested and will check back.
Best,
________________________________
From: Jakob Theorell <jakob.theorell using ndcn.ox.ac.uk<mailto:jakob.theorell using ndcn.ox.ac.uk>>
Sent: Monday, December 16, 2019 10:35 PM
To: Ahmed Metwally <ametwall using stanford.edu<mailto:ametwall using stanford.edu>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: Trigger a new build after version bump
Dear Ahmed,
I am not in the core team, but I still wonder: how long have you waited since you pushed? During the review process you get an immediate update of the package upon push with a version bump, but with accepted packages it takes 24-48 hours for the changes to trickle through to the build report. And you have to go in and check the build reports yourself on the BioConductor sites related to the release and devel branches.
Best regards
Jakob Theorell, MD/PhD
Autoimmune Neurology Group
Nuffield Department of Clinical Neurosciences
University of Oxford
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Ahmed Metwally <ametwall using stanford.edu<mailto:ametwall using stanford.edu>>
Sent: 17 December 2019 02:34
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Trigger a new build after version bump
Dear Bioc devel team,
OmicsLonDA package is failing to build on release and devel branches:
http://bioconductor.org/checkResults/release/bioc-LATEST/OmicsLonDA/
http://bioconductor.org/checkResults/devel/bioc-LATEST/OmicsLonDA/
I have fixed the issue and pushed the changes to RELEASE_3_10, and dev-master branch. I bumped the package version on the RELEASE_3_10 to v1.2.1 instead of v1.2.0. I did the same for the dev branch, bumped the version to v1.3.3 instead of v1.3.0. I was following instructions listed here: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
However, my changes didn't trigger a new build. In the past, when I was submitting the OmicsLonDA to Bioc, whenever I do version bump, I receive an email says that I successfully triggered a new build. This time I didn't receive any emails. Also, the build error and data don't change in the above-mentioned URLs to reflect a new build!
Please let me know what I'm missing here.
Thanks,
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