[Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis

[Alexey Sergushichev]

Herve, thanks! It seems I got it: there are no r-devel binaries for RSQLite
(https://cran.r-project.org/web/packages/RSQLite/index.html) so it's
installed from the sources as reactome.db, but not as AnnotationDbi. That's
why the installer doesn't know about dependency between reactome.db and
RSQLite. And this doesn't happen in bioc-release, because there is the
corresponding binary RSQLite package.

I understand that it's not specific to Bioconductor and is more appropriate
for r-devel list, right?

--
Alexey



On Fri, Mar 24, 2017 at 1:14 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Alexey,
>
> Based on the Travis build report, it looks like Travis used
> install.packages() to install reactome.db.
> What makes you think it used biocLite()?
>
> The problem seems to be related to the fact that reactome.db
> deps are divided in 2 groups: binary packages on one side and
> source packages on the other side. The installation procedure
> seems to treat each group separately and independently: binary
> packages first, and then source packages. This is flawed design
> to me, even if the "testing if installed package can be loaded"
> step is skipped when installing a binary package, which seems
> like an ostrich strategy to ignore possibly missing deps during
> the process.
>
> What's also puzzling with this Travis build report is that
> it looks like the binary packages were downloaded but not
> installed! This would explain why installation of reactome.db
> (source package) fails later (AnnotationDbi binary was downloaded
> but not installed). Flawed design "binaries first, then source
> packages" should actually work as long as (1) there is no attempt
> to load binary packages immediately after their installation and
> (2) the source packages are installed in topological order after
> all the binary packages have been installed.
>
> Cheers,
> H.
>
>
> On 03/23/2017 02:14 PM, Alexey Sergushichev wrote:
>
>> Hello all,
>>
>> I'm using travis for checking my project build and found something that
>> looks like a bug in how biocLite installs package dependencies. It appears
>> that at some point biocLite started to install them in an alphabet order,
>> not topological, and specifically on OS X.
>>
>> I've made a small dummy package to illustrate this: see
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&
>> r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_z
>> BnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=aNFQogh-gU_9sSF80iI9ROXy70
>> ayZvLrkPoKYiqGPQE&e=  and corresponding travis build
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-
>> 2Dci.org_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtB
>> cfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk5
>> 34I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=Pf3mEHAtHZHCN4WlB3cb3
>> 7Y2Wf_p2v_7mT2oBQGSIow&e= .
>>
>> There reactome.db package should be installed but fails on osx platform in
>> bioc-devel version. What happens there is reactome.db is installed before
>> RSQLite, while reactome.db dependes on RSQLite via AnnotationDbi (
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-
>> 2Dci.org_assaron_travis-2Dtest_jobs_214404313-23L630&d=
>> DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR
>> 1DU&s=369SlWBQZQV3iA3lfRmQ2DuAuMOuMtdbMzZaB9o9LV0&e= ). Compare it
>> with bioc-release version:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-
>> 2Dci.org_assaron_travis-2Dtest_jobs_214404316-23L543&d=
>> DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR
>> 1DU&s=chGtEiWkCYtswsgsZLMArKK67TI_MiX6sTgzLsc-v_c&e=  or bioc-devel
>> but on linux: https://urldefense.proofpoint.
>> com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest
>> _jobs_214389446-23L928&d=DwICAg&c=eRAMFD45gAfqt84VtBcfh
>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I
>> _zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=6REbwOP9lyEopleeq2Em9yxa
>> hQF6vA7iVVCkGw73Ick&e=
>>
>> Can anyone reproduce this behavior at their OS X machine? Is this bug in
>> biocLite or Travis?
>>
>> Best,
>> Alexey
>>
>>         [[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=DwICAg&c=eRAMFD45gAfqt
>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EC
>> GVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=HC5qJ-IF0Lmc4Qob
>> gJA8rfOpOHR9bWaF4MtFchvQma0&e=
>>
>>
> --
> 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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