Does the same hold for the pcxnData package? I can't see the RELEASE_3_6 as in pcxn.
-Sokratis On 31 October 2017 at 11:38, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > The latest version bump change you made to 0.99.27 was yesterday Oct 30 > right before we said to stop committing so we could make the release > branch. That change did make it into both the RELEASE_3_6 and the master > branch and should appear in the next build report for both versions. > > > Note: It can take 12-24 hours to see version bumps and changes on the > build report. The daily builders runs once per day to build all the > packages; while a version bump is absolutely required, it is not built > instantaneously on a version bump. > > > Please be sure to pull from upstream before making further changes as we > have bumped the versions in both the release and devel versions of packages > for the release. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk> > *Sent:* Tuesday, October 31, 2017 5:21:21 AM > *To:* Hervé Pagès > *Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel > *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and > fail build > > 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 >>> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g> >>> >>> [[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. 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<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. 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 >> <https://maps.google.com/?q=1100+Fairview+Ave.+N&entry=gmail&source=g>, >> 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 > <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g> > > 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. > -- 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
