[Bioc-devel] Bioconductor package landing pages
Hervé Pagès
hpages at fredhutch.org
Tue Sep 12 07:49:45 CEST 2017
Hi Nima,
The build machines are NOT trying to use version 1.0.0 of the
biotmleData package. They are using the version that is currently
publicly available here:
https://bioconductor.org/packages/3.6/data/experiment/html/biotmleData.html
It's version 1.1.0. The build machines installed it with just
biocLite("biotmleData"), like any user would. FWIW you can see all
the packages that are installed on the build machines by clicking
on the numbers in the "Installed pkgs" columns in the little table
at the top of the build report:
https://bioconductor.org/checkResults/3.6/bioc-LATEST/
The problem is that this version of biotmleData does not have the
rnaseqtmleOut dataset. This is easy to verify:
> library(BiocInstaller)
Bioconductor version 3.6 (BiocInstaller 1.27.4), ?biocLite for help
> biocLite("biotmleData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.4), R 3.4.0 Patched (2017-04-26
r72630).
Installing package(s) 'biotmleData'
trying URL
'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/biotmleData_1.1.0.tar.gz'
Content type 'application/x-gzip' length 30240432 bytes (28.8 MB)
==================================================
downloaded 28.8 MB
* installing *source* package 'biotmleData' ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (biotmleData)
The downloaded source packages are in
'/tmp/Rtmp6y3T4h/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> library(biotmleData)
> data(rnaseqtmleOut)
Warning message:
In data(rnaseqtmleOut) : data set 'rnaseqtmleOut' not found
Even though the dataset is now included in the *git source* of the
package, which is also at version 1.1.0, it seems that at the
time biotmleData 1.1.0 propagated to our public repo, it didn't
have it.
So all you need to do is bump biotmleData's version to 1.1.1.
Travis's Ubuntu, Appveyor, and your local machine (macOS) probably
use the git version of biotmleData so that's why biotmle builds there.
Having different versions of a package around that have the same version
number is always a source of *a lot* of confusion!
Hope this helps,
H.
On 09/10/2017 08:30 PM, Nima Hejazi wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.stat.berkeley.edu_-7Elaan_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=MTTWsO0CHDXNi2QEGOXXy6W3JoXnR8jmARpH95embb4&e=>
> | Hubbard Group
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__hubbard.berkeley.edu_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=1wPcpJEnKkTlWVvwSo3snmkolzodlq_4HV8thMQyQeo&e=>
> http://www.stat.berkeley.edu/~nhejazi
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat.berkeley.edu_-7Enhejazi&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=JjREjYmeoh3-mFCS4jDgd5TcPfqhYsfZX71QD6BXKWc&e=>
> http://nimahejazi.org
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__nimahejazi.org_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=0Ib9ncWCyvezv9EwAgxToXhyNwIXePUe9a-Lw8BYodg&e=> |
> Nima's blog
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__nimahejazi.org_blog_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=LgpvMqHhFGGQuu5ONvmoSNUFvHJ_EMht0ksaQFECWN0&e=>
>
> On Wed, Sep 6, 2017 at 9:15 AM, Hervé Pagès <hpages at fredhutch.org
> <mailto: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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.5_data-2Dexperiment-2DLATEST_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=mDW2T8DX9a7ih1OpihXfq0QpFhLig0EVcrr5Z-T1MGc&e=>
>
> and on the package landing page:
>
>
> https://bioconductor.org/packages/3.5/data/experiment/html/biotmleData.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.5_data_experiment_html_biotmleData.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=m5bkMpeBC8OWwE_Jo_duoxydLEvZ4mwVwxI0MmhYcew&e=>
>
> 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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_version-2Dnumbering_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2wRqRZa37y_UI111jV40ovpjdh4LfgSjLQBcpgsP_wc&s=w18Nz5ArlNGaTj9_sl0r2RDxazO6xYLMD9ej8ViRL3s&e=>
>
> 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=
> <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=
> <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=
> <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__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__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=
> <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=
> <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
> <mailto: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=
> <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 <mailto: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=
> <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=
> <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=
> <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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> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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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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