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_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@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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
