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_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
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>
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=
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| 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.tur...@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 <nhej...@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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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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