[Bioc-devel] Bioconductor package landing pages

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_wJYbW0WYiZvSXAJJKaaPhzWA&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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=u3lrjrrPopzPue9JmH71DSbjPoq1VnAuMUeoe1F_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_wJYbW0WYiZvSXAJJKaaPhzWA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=t-f3XRwcu1B2X5ECo1iYUwZwjyNuP8kQydG3IlkV1Og&e= >
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat.berkeley.edu_-7Enhejazi&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=BTn2lu5Zk5mBtu6-5sC843o83lkNN0Z1Ow9YF01YnkQ&e=
https://urldefense.proofpoint.com/v2/url?u=http-3A__nimahejazi.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=IEHeHRRW-yikdVb8REoffz9x1ca4MrOnjvXgXvYC_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=BK7q3XeAvimeWdGbWY_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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=9YlcDD3Gj1idpcDfRv909XLsL3YZwDSueYxrTqNA028&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_wJYbW0WYiZvSXAJJKaaPhzWA&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_wJYbW0WYiZvSXAJJKaaPhzWA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=t-f3XRwcu1B2X5ECo1iYUwZwjyNuP8kQydG3IlkV1Og&e= >
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat.berkeley.edu_-7Enhejazi&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=BTn2lu5Zk5mBtu6-5sC843o83lkNN0Z1Ow9YF01YnkQ&e=
https://urldefense.proofpoint.com/v2/url?u=http-3A__nimahejazi.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8mmx66fZ2EwKOSpTcbLrkO_QfbE24evQfZMzU-mtdaA&s=IEHeHRRW-yikdVb8REoffz9x1ca4MrOnjvXgXvYC_40&e= >

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