On Fri, Jul 5, 2013 at 1:40 PM, Kasper Daniel Hansen <kasperdanielhan...@gmail.com> wrote: > So what I saw yesterday (I think .. :) is that bumphunter was failing R CMD > check (it does not fail today) for version 1.1.7 (and earlier versions as > well) and still I was able to download the windows binary for 1.1.7. As I > understand it, that should be impossible since it failed R CMD check. >
If version 1.1.7 *ever* passed build and check, then it would get propagated. It seems that whatever causes the failure is transient (doesn't always happen). So that could cause this situation. Dan > Best, > Kasper > > > On Fri, Jul 5, 2013 at 4:37 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: >> >> On Fri, Jul 5, 2013 at 1:33 PM, Kasper Daniel Hansen >> <kasperdanielhan...@gmail.com> wrote: >> > My confusion is total. >> > >> > Suppose a package gets build (no errors) but fails check (error) and >> > gets a >> > version bump. Does the package source then get propagated to the >> > web/repository? >> > >> >> I'm confused by your question (sorry). >> From the point of view of the build system, build and check errors are >> the same. Both will prevent a package from being propagated to the >> web/repository. >> >> If a package fails check and then gets a version bump it will not >> propagate to the web, because presumably a mere version bump did not >> fix the problem that caused the check failure. >> >> Dan >> >> >> > Best, >> > Kasper >> > >> > >> > On Fri, Jul 5, 2013 at 3:29 PM, Dan Tenenbaum <dtene...@fhcrc.org> >> > wrote: >> >> >> >> On Thu, Jul 4, 2013 at 7:00 PM, Kasper Daniel Hansen >> >> <kasperdanielhan...@gmail.com> wrote: >> >> > So this thread is good for my follow up question. >> >> > >> >> > I am setting up a Windows box to test/fix bumphunter (newest version >> >> > 1.1.7) >> >> > which has been broken (R CMD check) for a while, especially on >> >> > Windows. >> >> > >> >> > This page (bottom) >> >> > http://bioconductor.org/packages/2.13/bioc/html/bumphunter.html >> >> > suggests that the latest binary version for Windows is 1.1.0 which is >> >> > also >> >> > probably the last time it build and checked properly. So this all >> >> > reflects >> >> > my expectations of not being able to get a binary version newer than >> >> > 1.1.0 >> >> > >> >> > However, when I install R-3.0.1 under windows, source biocLite and do >> >> > useDevel(TRUE) (getting BiocInstaller version 1.11.3) and then do >> >> > biocLite("bumphunter") >> >> > I get version 1.1.7. Why? I am asking for binary versions and nor >> >> > source. >> >> > >> >> >> >> The website wasn't being updated due to an unrelated issue. Fixed now. >> >> Dan >> >> >> >> >> >> > Best, >> >> > Kasper >> >> > >> >> > >> >> > On Sun, Jun 30, 2013 at 8:55 PM, Dan Tenenbaum <dtene...@fhcrc.org> >> >> > wrote: >> >> >> >> >> >> >> >> >> >> >> >> On Sunday, June 30, 2013, Kasper Daniel Hansen >> >> >> <kasperdanielhan...@gmail.com> wrote: >> >> >> > Doesn't this mean that the issue Wolfgang discusses only arises >> >> >> > when >> >> >> > people install from subversion? >> >> >> >> >> >> Yes. >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> > Kasper >> >> >> > >> >> >> > On Sun, Jun 30, 2013 at 6:56 PM, Martin Morgan >> >> >> > <mtmor...@fhcrc.org> >> >> >> > wrote: >> >> >> >> >> >> >> >> On 06/30/2013 03:32 PM, Dan Tenenbaum wrote: >> >> >> >>> >> >> >> >>> On Jun 30, 2013 12:43 PM, "Kasper Daniel Hansen" < >> >> >> >>> kasperdanielhan...@gmail.com> wrote: >> >> >> >>>> >> >> >> >>>> Also, as far as I understand, the package does not get build >> >> >> >>>> using >> >> >> >>>> the new >> >> >> >>>> commit, if it has already been build with that version number >> >> >> >>>> before. >> >> >> >>> >> >> >> >>> The package is built but not propagated to the web/repository. >> >> >> >>> This >> >> >> >>> "feature" allows developers to check that their changes get >> >> >> >>> built >> >> >> >>> by >> >> >> >>> the >> >> >> >> >> >> >> >> It's more a safety measure -- if the developer FORGETS to bump, >> >> >> >> then >> >> >> >> at >> >> >> >> least we are not distributing two implementations under the same >> >> >> >> version >> >> >> >> number. >> >> >> >> >> >> >> >> As Wolfgang says, version numbers are free so no need to hold >> >> >> >> back >> >> >> >> on >> >> >> >> their use. >> >> >> >> >> >> >> >> Martin >> >> >> >> >> >> >> >>> build system, but yes, once you're satisfied that things work, >> >> >> >>> you >> >> >> >>> should >> >> >> >>> bump the version number to propagate the package and avoid the >> >> >> >>> confusion >> >> >> >>> Wolfgang describes. >> >> >> >>> >> >> >> >>> Dan >> >> >> >>> >> >> >> >>> >> >> >> >>>> >> >> >> >>>> Best, >> >> >> >>>> Kasper >> >> >> >>>> >> >> >> >>>> >> >> >> >>>> On Sun, Jun 30, 2013 at 3:12 AM, Wolfgang Huber >> >> >> >>>> <whu...@embl.de> >> >> >> >>>> wrote: >> >> >> >>>> >> >> >> >>>>> Hi All, >> >> >> >>>>> >> >> >> >>>>> just a reminder that it is good practice to bump up the >> >> >> >>>>> package >> >> >> >>>>> version >> >> >> >>>>> when you commit a change to a package's source, even if you >> >> >> >>>>> consider >> >> >> >>>>> it >> >> >> >>>>> 'trivial'. Version numbers are free, while the confusion >> >> >> >>>>> ensuing >> >> >> >>>>> from >> >> >> >>> >> >> >> >>> there >> >> >> >>>>> >> >> >> >>>>> being different versions of the software with ostensibly the >> >> >> >>>>> same >> >> >> >>> >> >> >> >>> version >> >> >> >>>>> >> >> >> >>>>> can waste a great deal of someone's time. >> >> >> >>>>> >> >> >> >>>>> Dan / Bioc-Core team: would it be good to mention this >> >> >> >>>>> somewhere >> >> >> >>>>> on >> >> >> >>>>> http://bioconductor.org/developers/source-control ? >> >> >> >>>>> >> >> >> >>>>> Best wishes >> >> >> >>>>> Wolfgang >> >> >> >>>>> _______________________________________________ >> >> >> >>>>> Bioc-devel@r-project.org mailing list >> >> >> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >>>>> >> >> >> >>>> >> >> >> >>>> [[alternative HTML version deleted]] >> >> >> >>>> >> >> >> >>>> _______________________________________________ >> >> >> >>>> Bioc-devel@r-project.org mailing list >> >> >> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >>> >> >> >> >>> [[alternative HTML version deleted]] >> >> >> >>> >> >> >> >>> _______________________________________________ >> >> >> >>> Bioc-devel@r-project.org mailing list >> >> >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Computational Biology / Fred Hutchinson Cancer Research Center >> >> >> >> 1100 Fairview Ave. N. >> >> >> >> PO Box 19024 Seattle, WA 98109 >> >> >> >> >> >> >> >> Location: Arnold Building M1 B861 >> >> >> >> Phone: (206) 667-2793 >> >> >> > >> >> >> > >> >> > >> >> > >> > >> > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
