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 <[email protected]> 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]] >> >> _______________________________________________ >> [email protected] 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: [email protected] > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
