[Bioc-devel] Bioconductor package landing pages
Hi Herv?, 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, Herv? Pag?s <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]]
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-- Herv? Pag?s 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