----- Original Message ----- > From: "Martin Morgan" <martin.mor...@roswellpark.org> > To: "Glyn Bradley" <glyn.x.brad...@gsk.com>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Tuesday, March 22, 2016 6:03:56 AM > Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR)
> On 03/22/2016 07:53 AM, Glyn Bradley wrote: >> Hi, >> We’ve got CausalR back up both in the 3.2 release and devel, but although we >> committed the same package (with different version number) to both release >> and >> devel, the landing pages are showing >> build:OK in release but build:warnings in devel. >> >> Does anyone know why this might be, and more importantly, would the >> build:warnings in devel affect the release of the package in v3.3? >> > > Clicking on the 'build' shield at the top of your package landing page > takes you to the build report for your package > > http://bioconductor.org/checkResults/devel/bioc-LATEST/CausalR/ > > Clicking on one of the 'WARNING' tags takes you to the build report for > that platform, and scrolling down we see > > * checking whether package ‘CausalR’ can be installed ... [1s/1s] WARNING > Found the following significant warnings: > Warning: Package 'CausalR' is deprecated and will be removed from > Bioconductor > See ‘/home/biocbuild/bbs-3.3-bioc/meat/CausalR.Rcheck/00install.out’ for > details. > > Your package was marked for deprecation (usually because there were > errors that prevented it from building that persisted for a long time, > leading us to think that the maintainer had abandoned it). Now that the > package has built, the deprecation tag will be (manually, by 'us') > removed and the warning will go away. We will remove the deprecation tag. > This is a bit puzzling as the tag was removed from both release and devel on 3/18. Perhaps there is an installed version of the package on one or more build machines that is still marked as deprecated. I will take a look. Dan > More generally, bioc-release uses the version of R and other Bioc > packages that are available to users of the release version of R and > Bioconductor, whereas bioc-devel uses the version of R and other Bioc > packages that will be available when the next bioc release occurs. For > instance, this means that bioc release currently uses R-3.2.4, whereas > bioc-devel uses R-devel / 3.3.0. > > Martin > >> Thanks, >> Glyn >> >> From: Glyn Bradley >> Sent: 16 March 2016 13:22 >> To: 'Kasper Daniel Hansen' >> Cc: bioc-devel@r-project.org >> Subject: RE: [Bioc-devel] Issues uploading our updated package (CausalR) >> >> Thanks, we’ve already read that. >> I was more hoping for a response from the Bioconductor team >> Glyn >> >> From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com] >> Sent: 16 March 2016 13:20 >> To: Glyn Bradley >> Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> >> Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR) >> >> I don't know much about deprecated packages and how to deal with them, but >> for >> your svn questions, start by reading the howto: >> >> https://www.bioconductor.org/developers/source-control/ >> >> Kasper >> >> On Wed, Mar 16, 2016 at 6:19 AM, Glyn Bradley >> <glyn.x.brad...@gsk.com<mailto:glyn.x.brad...@gsk.com>> wrote: >> Hi All, >> >> Our package, CausalR, broke when igraph was updated last year. We have now >> fixed >> this, but are having problems uploading the >> new version. The package had become depreciated in devel, but there's still a >> landing page in release. >> >> We checked out the existing Bioconductor version (via SVN) to a local >> directory >> from >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR >> The new, fixed, version was uploaded via SVN commit [Revision: 114806*] back >> to >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR >> >> But if you open >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR in a web >> browser >> it's still showing old data from Revision: 114827 (we don't understand why >> our >> new upload had a revision number lower >> than this) >> >> Also, because CausalR had become depreciated in devel, we were previously >> told >> we would have to update the package >> in both the devel and release trunks, but we only have the one url >> (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR) >> So separately to the issues above about our update not seeming to stay on the >> system, could someone please advise how we >> update both trunks? >> >> Many thanks. Feel free to email me directly if this isn't a suitable >> discussion >> for the mailing list. >> Glyn >> >> >> >> >> ________________________________ >> >> This e-mail was sent by GlaxoSmithKline Services Unlimited >> (registered in England and Wales No. 1047315), which is a >> member of the GlaxoSmithKline group of companies. The >> registered address of GlaxoSmithKline Services Unlimited >> is 980 Great West Road, Brentford, Middlesex TW8 9GS. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> ________________________________ >> >> This e-mail was sent by GlaxoSmithKline Services Unlimited >> (registered in England and Wales No. 1047315), which is a >> member of the GlaxoSmithKline group of companies. The >> registered address of GlaxoSmithKline Services Unlimited >> is 980 Great West Road, Brentford, Middlesex TW8 9GS. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > 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. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
