I see! Thanks for letting me know, Martin. Best, ________________________________ From: Martin Morgan <mtmorgan.b...@gmail.com> Sent: Friday, December 20, 2019 2:20 PM To: Ahmed Metwally <ametw...@stanford.edu>; Shepherd, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Trigger a new build after version bump
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 <ametw...@stanford.edu> Date: Friday, December 20, 2019 at 5:08 PM To: Martin Morgan <mtmorgan.b...@gmail.com>, "Shepherd, Lori" <lori.sheph...@roswellpark.org> Cc: "bioc-devel@r-project.org" <bioc-devel@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.b...@gmail.com> Sent: Thursday, December 19, 2019 12:19 PM To: Ahmed Metwally <ametw...@stanford.edu>; Shepherd, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@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-boun...@r-project.org on behalf of ametw...@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-boun...@r-project.org> on behalf of Ahmed Metwally <ametw...@stanford.edu> Sent: Tuesday, December 17, 2019 4:58 AM To: Shepherd, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@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.sheph...@roswellpark.org<mailto:lori.sheph...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Ahmed Metwally <ametw...@stanford.edu<mailto:ametw...@stanford.edu>> Sent: Tuesday, December 17, 2019 2:49 AM To: Jakob Theorell <jakob.theor...@ndcn.ox.ac.uk<mailto:jakob.theor...@ndcn.ox.ac.uk>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@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.theor...@ndcn.ox.ac.uk<mailto:jakob.theor...@ndcn.ox.ac.uk>> Sent: Monday, December 16, 2019 10:35 PM To: Ahmed Metwally <ametw...@stanford.edu<mailto:ametw...@stanford.edu>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Ahmed Metwally <ametw...@stanford.edu<mailto:ametw...@stanford.edu>> Sent: 17 December 2019 02:34 To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@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. 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