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

Hervé Pagès hpages at fredhutch.org
Thu Mar 23 23:14:57 CET 2017

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.


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_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=aNFQogh-gU_9sSF80iI9ROXy70ayZvLrkPoKYiqGPQE&e=  and corresponding travis build
> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=Pf3mEHAtHZHCN4WlB3cb37Y2Wf_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_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&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_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=6REbwOP9lyEopleeq2Em9yxahQF6vA7iVVCkGw73Ick&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.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=HC5qJ-IF0Lmc4QobgJA8rfOpOHR9bWaF4MtFchvQma0&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

More information about the Bioc-devel mailing list