[Bioc-devel] svn and package version numbers

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.

Best,
Kasper


On Fri, Jul 5, 2013 at 4:37 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

On Fri, Jul 5, 2013 at 1:33 PM, Kasper Daniel Hansen
<kasperdanielhansen at 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 <dtenenba at fhcrc.org>
wrote:

On Thu, Jul 4, 2013 at 7:00 PM, Kasper Daniel Hansen
<kasperdanielhansen at 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 <dtenenba at fhcrc.org>
wrote:

On Sunday, June 30, 2013, Kasper Daniel Hansen
<kasperdanielhansen at 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
<mtmorgan at fhcrc.org>
wrote:

On 06/30/2013 03:32 PM, Dan Tenenbaum wrote:

On Jun 30, 2013 12:43 PM, "Kasper Daniel Hansen" <
kasperdanielhansen at 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
<whuber at 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

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