Fair enough (for other readers: Dan and I are having some private correspondance about this error, and currently we believe it to be random/transient).
Kasper On Fri, Jul 5, 2013 at 4:46 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > 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 > >> >> >> > > >> >> >> > > >> >> > > >> >> > > >> > > >> > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
