The name of my package is icetea. Here's the link <https://github.com/Bioconductor/Contributions/issues/719> to the submission. I checked today and VariantAnnotation build was passing now, so simply re-pushed with bumped version and it worked! (well not exactly, I still have the RSubread issue with windows that I mentioned last week, but at least VariantAnnotation is not throwing errors).
@Hervé Regarding the issue with RSubread, I tried adding the .BBSoptions file in the package source dir. Although I added this file under .Rbuildignore as well to avoid R CMD check complaining about non-standard dir. It didn't work. Thanks for the input everyone. Best, Vivek On 5/30/18 7:31 PM, Hervé Pagès wrote: > Hi Vivek, > > Are you submitting a package and bumped its version in order to trigger > a new build? The build system used for the submission is the "Single > Package Builder" (SPB) and is not the same as the main builder used > for the daily builds (BBS). It would help if you could provide the link > to the build report where you see the error or at least the name of > your package. > > On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote: >> >> The package throwing error is*VariantAnnotation *(coming from function: >> locateVariants). I checked it's build for the dev branch and indeed it's >> broken. ** >> >> All right then I would remove version specification from my package and >> I guess I'll wait for**VariantAnnotation to get fixed. > > FWIW the latest version of VariantAnnotation in devel is 1.27.1: > > https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html > > and it passes BUILD and CHECK today on all platforms today. > > The SPB sometimes needs to install dependencies that in some rare > occasion can get stale a few days later. So in a sense yes it can > cache packages. Lori, our SPB expert, will be able to help you with > this if you provide the name of your package. Thanks! > > H. > >> >> Best, >> Vivek >> >> >> >> On 05/30/2018 04:04 PM, Martin Morgan wrote: >>> There is no cache; like users you get the 'current' version of the >>> package from the relevant repository. If your package used >>> concatenateObjects, then it needs to be updated. If your package is >>> broken through a third package, it needs to be fixed (perhaps it has >>> been but did not propagate, see the build reports for packages in the >>> devel branch >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc&s=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk&e= >>> >>> , and look for the >>> stoplight at the right). >>> >>> Martin >>> >>> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote: >>>> Hi All >>>> >>>> Is there any build cache on bioc build system? I updated S4Vector and >>>> IRanges in my dependencies and triggered a new build of my package, >>>> only >>>> to find that this broke other dependencies due to renaming of function >>>> `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the >>>> mentioned versions in my DESCRIPTION, but the build is still broken. >>>> Also tried specifying a particular version of these packages and I get >>>> the error : >>>> >>>> ** byte-compile and prepare package for lazy loading Error in >>>> loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = >>>> vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == >>>> 2.14.10 >>>> is required >>>> >>>> How do I refresh the cache? >>>> >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the >>> employee or agent responsible for the delivery of this message to the >>> intended recipient(s), you are hereby notified that any disclosure, >>> copying, distribution, or use of this email message is prohibited. If >>> you have received this message in error, please notify the sender >>> immediately by e-mail and delete this email message from your >>> computer. Thank you. >> >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
