Hi all, There was an error in the pcxn package (and pcxnData as a resut of not finding pcxn since it didnt build) which I fixed yesterday morning, but it doesnt seem to accept my changes as the version in the build report is not the last one I created but the erroneous one (2 days ago). I checked the upstream of my package and it has my latest changes.
Regards, Sokratis On 27 October 2017 at 16:57, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi guys, > > On 10/27/2017 05:50 AM, Obenchain, Valerie wrote: > >> Hi Sokratis, >> >> I added the .BBSoptions file to pcxn when it should have been added to >> pcxnData. The .BBSoptions file should be put in the package that 'Suggests' >> (not 'Depends') on the other. In this case it's pcxnData that needs the >> .BBSoptions. Sorry for the mix up, this has been fixed. >> >> The data package should install with today's builds and be clean on the >> Saturday report. The software package should then install with the Saturday >> builds and be clean on the Sunday report. >> >> > This is what should happen: > > - pcxnData should install with today's data-exp builds (they > started this morning) but vignette will still fail (pcxn still > missing) > > - pcxn won't install (will be back to NotNeeded) but should pass > build/check and propagate on Saturday afternoon > > - on Sunday morning, the data exp builds will find pcxn **on line** > (because now it propagated) so will be able to install it so > vignette will finally build and the package will propagate > > Thanks for taking care of this, > > H. > > Valerie >> >> >> On 10/26/2017 04:26 AM, Shepherd, Lori wrote: >> >> We have already taken care of this on our end and you shouldn't need to >> do anything else. As always changes reflected may take a few days to >> reflect in the build reports. >> >> >> The solution is to add a .BBSoptions file with ForceInstall: TRUE to the >> software package. Since there is a circular dependency this will force >> install the software package even though there will be ERRORs because of >> the missing data package. On the next build of the data packages, the data >> package will then successfully build finding the software package. Then >> following, the software package will also build finding the data package. >> >> >> Cheers, >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> 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 Sokratis Kariotis < >> s.kario...@sheffield.ac.uk><mailto:s.kario...@sheffield.ac.uk> >> Sent: Thursday, October 26, 2017 4:02:53 AM >> To: bioc-devel >> Subject: [Bioc-devel] Accepted packages can't find each other and fail >> build >> >> Hey all, >> >> I created 2 packages that got accepted (pcxn and pcxnData) where pcxn >> depends on the data coming from pcxnData. However, in the vignettes of >> pcxnData I am using library(pcxn) to demonstrate what can you do with the >> data. As a result both packages fail building in BioC 3.6 as they can't >> find each other. In a previous pair of packages I am maintaining >> (pathprint >> and pathprintGEOData) I could use the first library in the data package >> vignette and building was fine. Is it necessary to remove library(pcxn) >> from pcxnData to get them build? Thanks in advance! >> >> Cheers >> -- >> Sokratis Kariotis >> Scientific Programmer >> Hidelab >> Sheffield Institute for Translational Neuroscience >> 385a Glossop Rd, Sheffield, S10 2HQ >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Fl >> PSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04Qg >> ZwXutO5Ss-V-ZqiQSgw3JctMdgs&e= >> >> >> This email message may contain legally privileged and/or confidential >> information. 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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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Fl >> PSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04Qg >> ZwXutO5Ss-V-ZqiQSgw3JctMdgs&e= >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sokratis Kariotis Scientific Programmer Hidelab Sheffield Institute for Translational Neuroscience 385a Glossop Rd, Sheffield, S10 2HQ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
