[Bioc-devel] LOBSTAHS dev build failing on toluca2; version does not update in devel

Thu Jan 26 23:20:34 CET 2017

Hi,

Just to clarify, we do have daily software builds that start at 2:15pm
PST. We did not have a devel build report this week on Tuesday, Jan 24
due to a problem with the postrun script. AFAIK that is the only day
this week we haven't had a full build report.

Looking at the svn logs for LOBSTAHS in devel, there were quite a few
commits on Jan 25. About 1/3 were before the 2:25pm deadline. These were
probably the commits that straddled the deadline:

------------------------------------------------------------------------
r126164 | j.collins | 2017-01-25 14:34:52 -0800 (Wed, 25 Jan 2017) | 1 line

Merge branch 'master' of https://github.com/Bioconductor-mirror/LOBSTAHS
into devel
------------------------------------------------------------------------
r126159 | j.collins | 2017-01-25 13:56:09 -0800 (Wed, 25 Jan 2017) | 1 line

Remove .tar files

So the package picked up by the builds was r126159. If we check this
revision out of svn

  svn co -r126159 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LOBSTAHS

and look at the DESCRIPTION file the version is 1.1.1. So that version
was picked up yesterday for today's builds. The new build report just
posted for Jan 26 (which started Jan 25 at 2:25pm PST) and it is again
showing version 1.1.1 as we would expect.

It looks like you bumped the version in -r126221 but made several
changes after that. It's good practice to bump the version as part of
your final commit. When you don't, the version doesn't really represent
a snapshot of  the package - you have drift here over 5 commits, all
with the same version. The version bump is the trigger that refreshes /
posts to the package landing page so it's important to bump as part of
your final commit.

------------------------------------------------------------------------
r126225 | j.collins | 2017-01-25 14:58:22 -0800 (Wed, 25 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/LOBSTAHS/README.md

Reversing the stylistic edit
------------------------------------------------------------------------
r126224 | j.collins | 2017-01-25 14:58:15 -0800 (Wed, 25 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/LOBSTAHS/README.md

Stylistic edit
------------------------------------------------------------------------
r126223 | j.collins | 2017-01-25 14:58:08 -0800 (Wed, 25 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/LOBSTAHS/README.md
   M /trunk/madman/Rpacks/LOBSTAHS/man/LOBdbase.Rd
   M /trunk/madman/Rpacks/LOBSTAHS/man/LOBdefaults.Rd
   M /trunk/madman/Rpacks/LOBSTAHS/man/doLOBscreen.Rd
   M /trunk/madman/Rpacks/LOBSTAHS/man/generateLOBdbase.Rd
   M /trunk/madman/Rpacks/LOBSTAHS/vignettes/LOBSTAHS.Rmd

Adding Fulton E. hux. paper to references throughout package
------------------------------------------------------------------------
r126222 | j.collins | 2017-01-25 14:57:56 -0800 (Wed, 25 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/LOBSTAHS/data/default.LOBdbase.RData

Commit updated default database
------------------------------------------------------------------------
r126221 | j.collins | 2017-01-25 14:57:47 -0800 (Wed, 25 Jan 2017) | 1 line
Changed paths:
   M /trunk/madman/Rpacks/LOBSTAHS/DESCRIPTION

Bump version, date

The builds tomorrow should post results for 1.1.3.

Valerie

On 01/26/2017 11:05 AM, Kasper Daniel Hansen wrote:
> Traditionally we have had daily builds, which then takes more than 12h to
> complete.  Recently, the daily build schedule has been more intermitten - I
> don't know for sure but I thought we were back to daily builds.
>
> Still, there can be a big delay due to build time and start, like up to
> 36h.  But it is 1.1.3 in subversion, so I think it is a build delay.
>
> On Thu, Jan 26, 2017 at 11:04 AM, James Collins <
> james.r.collins at aya.yale.edu> wrote:
>
>> Thanks, Kasper. On your second point: Yes, several recent updates. The
>> bump to v1.1.2 was two days ago, so I figured that would have been
>> reflected in a newer build already. I will give it a few more days.
>> Jamie
>>
>>
>> On Jan 26, 2017, at 11:57 AM, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>>
>> It happens in devel that your dependencies fail and then your package
>> fails.  Right now XCMS fails in devel because mzR fails.  That will
>> presumably be sorted out.
>>
>> The latest build report
>>   http://bioconductor.org/checkResults/3.5/bioc-LATEST/LOBSTAHS/
>> is 1.1.1.  Did you do a couple of updates very recently - remember the
>> build system gets run (at most) daily.
>>
>> Best,
>> Kasper
>>
>> On Thu, Jan 26, 2017 at 9:53 AM, James Collins <james.r.collins at aya.
>> yale.edu> wrote:
>>
>>> Hi all:
>>>
>>> Two questions regarding the LOBSTAHS package:
>>>
>>> 1. Dev build seems to be failing (“error”) on toluca2 after I pushed some
>>> updates from our git repository to Bioc svn. Error is:
>>> * installing to library ‘/Library/Frameworks/R.framewo
>>> rk/Versions/3.4/Resources/library’
>>> ERROR: dependencies ‘xcms’, ‘CAMERA’ are not available for package
>>> ‘LOBSTAHS’
>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/
>>> library/LOBSTAHS’
>>> However, seems to build fine on oaxaca. Any ideas why this is happening?
>>> xcms and CAMERA should be available for the package, correct?
>>>
>>> 2. After bumping the version number (from 1.1.1 to 1.1.2 and then 1.1.3)
>>> with the updates, the latest version (1.1.3) does not appear to be showing
>>> on the dev page, which leads me to believe it is not the version being
>>> disseminated with biocLite()
>>>
>>> http://bioconductor.org/packages/3.5/bioc/html/LOBSTAHS.html <
>>> http://bioconductor.org/packages/3.5/bioc/html/LOBSTAHS.html>
>>>
>>> Perhaps this is because I cherry-pick all my commits when committing from
>>> git to the Bioc svn? Or because of the error message?
>>>
>>> Thanks in advance!
>>>
>>> Jamie Collins
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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