[Bioc-devel] Bioconductor package landing pages

Nima Hejazi nhejazi at berkeley.edu
Mon Sep 11 05:30:35 CEST 2017 

Hi Hervé,

Thanks for your note. I do indeed believe that the error was initially due
to the build trying to use an older version of the data package biotmleData
(1.0.0, as you stated). After the update of biotmleData (to 1.1.0; aside: I
realize this is rather bad practice, but I don't intend to update the data
package frequently at all -- hopefully never after the next release), the
package biotmle ought to be building properly. In fact, as far as I can
tell there might some kind of issue related to caching in the Bioconductor
build because

1) biocLite is installing v.1.1.0 of biotmleData, which is the version
required to properly build biotmle
2) independent builds are passing on all systems: Travis's Ubuntu,
Appveyor, and my local machine (macOS)
3) I bumped the version of biotmle last week but even the most recent build
(as of 09 September) is still failing, due to trying to use v.1.0.0 of
biotmleData

Is there something more I should be doing to fix the build? Thanks in
advance for your help.

Warm Regards,
— Nima Hejazi

--
Nima Hejazi
Doctoral Student
Division of Biostatistics
University of California, Berkeley
van der Laan Group <https://www.stat.berkeley.edu/~laan/> | Hubbard Group
<http://hubbard.berkeley.edu/>
http://www.stat.berkeley.edu/~nhejazi
http://nimahejazi.org | Nima's blog <http://nimahejazi.org/blog/>

On Wed, Sep 6, 2017 at 9:15 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Nima,
>
> Normally you have to allow 24 hours or so to see your changes show up
> on the build report:
>
>   https://bioconductor.org/checkResults/3.5/data-experiment-LATEST/
>
> and on the package landing page:
>
>
> https://bioconductor.org/packages/3.5/data/experiment/html/
> biotmleData.html
>
> But sometimes more if our build system was not able to complete the
> builds.
>
> The package version you see on the package landing page is the one
> you'll get via biocLite(). Right now, when I do biocLite("biotmleData")
> in BioC release, I get biotmleData 1.1.0. When you tried this yesterday
> maybe you got version version 1.0.0 because version 1.1.0 hadn't
> propagated yet.
>
> BTW bumping the version from 1.0.0 to 1.1.0 in release is not a good
> idea. You should only bump the z part of the x.y.z version when you make
> changes in release. See
>
>   https://bioconductor.org/developers/how-to/version-numbering/
>
> for more information on this.
>
> Cheers,
> H.
>
> On 09/05/2017 11:56 AM, Nima Hejazi wrote:
>
>> Hi Nitesh --
>>
>> Thanks very much for the help on this last week. I've been investigating
>> the build problem displayed on the page you linked rather slowly but have
>> reached a point where I now have a question:
>>
>>     - The error appears to be due to an example data set not being found.
>>     This data set appears in the biotmleData package on Bioc. I've updated
>>     biotmleData on both the master and RELEASE_3_5 branches to now
>> contain that
>>     data set, but when I install biotmleData via biocLite, I still get
>> version
>>     1.0.0 -- even though RELEASE_3_5 now contains 1.1.0 -- is there
>> something
>>     that I am missing here?
>>     - The GitHub repos for biotmle <https://urldefense.proofpoint
>> .com/v2/url?u=https-3A__github.com_nhejazi_biotmle&d=
>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-
>> mtdaA&s=9YlcDD3Gj1idpcDfRv909XLsL3YZwDSueYxrTqNA028&e= > and
>>     biotmleData <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>> github.com_nhejazi_biotmleData&d=DwIGaQ&c=eRAMFD45gAfqt84VtB
>> cfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66f
>> Z2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=u3lrjrrPopzPue9JmH71D
>> SbjPoq1VnAuMUeoe1F_WaE&e= > contain both the
>>     master and RELEASE_3_5 branch, both of which appear to be fully
>>     synced/updated wrt to Bioconductor (i.e., "git pull bioc RELEASE_3_5"
>>     returns "Everything up-to-date"), so I don't believe this to be a sync
>>     issue.
>>
>>
>> ​Any help in resolving this issue would be much appreciated.​​
>>
>> Warm Regards,
>> — Nima Hejazi
>>
>> --
>> Nima Hejazi
>> Doctoral Student
>> Division of Biostatistics
>> University of California, Berkeley
>> van der Laan Group <https://urldefense.proofpoint
>> .com/v2/url?u=https-3A__www.stat.berkeley.edu_-7Elaan_&d=
>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-
>> mtdaA&s=x8GhbJbVSpx7qQOlLfUK4_ja-UIQqMdTomPAmUEBmNk&e= > | Hubbard Group
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__
>> hubbard.berkeley.edu_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK
>> 7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpT
>> cbLrkO_QfbE24evQfZMzU-mtdaA&s=t-f3XRwcu1B2X5ECo1iYUwZwjyNuP8
>> kQydG3IlkV1Og&e= >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat
>> .berkeley.edu_-7Enhejazi&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2E
>> wKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=BTn2lu5Zk5mBtu6-5sC843
>> o83lkNN0Z1Ow9YF01YnkQ&e=
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__nimaheja
>> zi.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbW
>> Y_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24ev
>> QfZMzU-mtdaA&s=9SgIZVMQy8w6hOO7ApRH-bDkc6CwLS8QSTp-diDl5yA&e=  | Nima's
>> blog <https://urldefense.proofpoint.com/v2/url?u=http-3A__
>> nimahejazi.org_blog_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7
>> q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTc
>> bLrkO_QfbE24evQfZMzU-mtdaA&s=IEHeHRRW-yikdVb8REoffz9x1ca4MrO
>> njvXgXvYC_40&e= >
>>
>> On Mon, Aug 28, 2017 at 11:58 AM, Turaga, Nitesh <
>> Nitesh.Turaga at roswellpark.org> wrote:
>>
>> Hi Nima,
>>>
>>> Please check https://urldefense.proofpoint.
>>> com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_
>>> bioc-2DLATEST_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAv
>>> imeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_
>>> QfbE24evQfZMzU-mtdaA&s=Utq-cY0IaWdeVTBbsfkOjDpn84D1xDqKaheeHXmgbNc&e=
>>> biotmle/malbec1-buildsrc.html, it shows that the page was generated on
>>> Sunday. There is also a snapshot date when your repo was captured by the
>>> nightly build, and even the last commit.
>>>
>>> But this issue, is because your package has an ERROR, and there hasn’t
>>> been a version bump.
>>>
>>> Best,
>>>
>>> Nitesh
>>>
>>>
>>>
>>> On Aug 28, 2017, at 2:48 PM, Nima Hejazi <nhejazi at berkeley.edu> wrote:
>>>>
>>>> Hello All ---
>>>>
>>>> After the relatively recent migration from SVN to git, I've followed the
>>>> various guidelines for linking the GitHub repo
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>> github.com_nhejazi_biotmle&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
>>>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2E
>>>> wKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=9YlcDD3Gj1idpcDfRv909X
>>>> LsL3YZwDSueYxrTqNA028&e= > of my package biotmle to the
>>>> Bioconductor git server, I've pushed several important updates to the
>>>>
>>> Bioc
>>>
>>>> master branch.
>>>>
>>>> My understanding is that the master branch represents the development
>>>> version (in contrast to RELEASE_3_5). That said, it appears that the
>>>>
>>> package
>>>
>>>> landing page for the Bioc development version
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
>>>> bioconductor.org_packages_devel_bioc_html_biotmle.html&
>>>> d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW
>>>> 0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-
>>>> mtdaA&s=GbClVUyh6jrp_sWbrGF_QRviL57GEEPl2z2E5LpN4e0&e= >
>>>>
>>> does
>>>
>>>> not reflect the current status of the master branch of the Bioc git
>>>>
>>> history.
>>>
>>>>
>>>> Perhaps I am missing something simple? Any help would be much
>>>>
>>> appreciated.
>>>
>>>>
>>>> Warm Regards,
>>>> — Nima Hejazi
>>>>
>>>> --
>>>> Nima Hejazi
>>>> Doctoral Student
>>>> Division of Biostatistics
>>>> University of California, Berkeley
>>>> van der Laan Group <https://urldefense.proofpoint
>>>> .com/v2/url?u=https-3A__www.stat.berkeley.edu_-7Elaan_&d=
>>>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>>>> YiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-
>>>> mtdaA&s=x8GhbJbVSpx7qQOlLfUK4_ja-UIQqMdTomPAmUEBmNk&e= > | Hubbard
>>>>
>>> Group
>>>
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__
>>>> hubbard.berkeley.edu_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK
>>>> 7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpT
>>>> cbLrkO_QfbE24evQfZMzU-mtdaA&s=t-f3XRwcu1B2X5ECo1iYUwZwjyNuP8
>>>> kQydG3IlkV1Og&e= >
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat
>>>> .berkeley.edu_-7Enhejazi&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
>>>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2E
>>>> wKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=BTn2lu5Zk5mBtu6-5sC843
>>>> o83lkNN0Z1Ow9YF01YnkQ&e=
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__nimaheja
>>>> zi.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbW
>>>> Y_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24ev
>>>> QfZMzU-mtdaA&s=9SgIZVMQy8w6hOO7ApRH-bDkc6CwLS8QSTp-diDl5yA&e=  |
>>>> Nima's blog <https://urldefense.proofpoint.com/v2/url?u=http-3A__
>>>> nimahejazi.org_blog_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7
>>>> q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTc
>>>> bLrkO_QfbE24evQfZMzU-mtdaA&s=IEHeHRRW-yikdVb8REoffz9x1ca4MrO
>>>> njvXgXvYC_40&e= >
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt
>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8m
>>>> mx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=U0_dzOn2mTogJs3n
>>>> 5GXGqOeiiF1Wn_iOTUYQ4elmdeg&e=
>>>>
>>>
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>>
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>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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