[Bioc-devel] New Mac builder and availability of Mac binary packages
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Sat Apr 11 07:34:20 CEST 2020
On 4/10/20 17:22, Yang,Peng wrote:
> Hi Herve,
>
> Ok, I will use the condition to disable OpenMP for Mac OS.
> And I need to push it into the devel branch before Apr 24th? Just make sure that I understand it right.
Yes, before Apr 24th. See our release schedule here:
https://bioconductor.org/developers/release-schedule/
Thanks,
H.
>
> Thanks,
> Peng
>
> On 4/10/20, 7:13 PM, "Hervé Pagès" <hpages using fredhutch.org> wrote:
>
> On 4/10/20 16:54, Yang,Peng wrote:
> > Hi Herve,
> >
> > Thank you so much for hearing back from you.
> >
> > Actually we are thinking to switch OpenMP into MPI or other API, which is supported by R 4.0.0; however, it may take us for a while.
> > In the meantime, I have noticed that the scheduled time to release R 4.0.0 is on Friday April 24th, so do we have to finish our package before that time?
> > If we are not be able to finish it by then, can we choose the first option and push our updated package whenever we are done with the API switching?
>
> Yes, the first option (use conditionals to disable OpenMP on macOS) is
> probably your best option for now. Thanks for taking care of this.
>
> Best,
> H.
>
> >
> > Thanks,
> > Peng
> >
> > On 4/10/20, 12:31 PM, "Hervé Pagès" <hpages using fredhutch.org> wrote:
> >
> > Hi Peng,
> >
> > You cannot "push" binaries. DeMixT has a compilation error (+ some
> > imporant warnings) that seem to be caused by the use of OpenMP in its C
> > code. Unfortunately, starting with R 4.0.0, R no longer supports OpenMP
> > on macOS.
> >
> > You basically have 3 options, from best to worst:
> > 1. use conditionals to disable OpenMP on macOS;
> > 2. drop OpenMP completely (i.e. on all platforms);
> > 3. do nothing and we'll mark the package as unsupported on macOS.
> >
> > Thanks,
> > H.
> >
> > On 4/9/20 20:17, Yang,Peng wrote:
> > > Dear Bioconductor team,
> > >
> > > I just found out that our package DeMixT 1.3.5 is failed to install for Mac under the developed version.
> > >
> > > Does that mean I need to rebuild the package under the official Mac build of R 4.0.0 alpha and push it again?
> > >
> > > Thanks,
> > > Peng
> > >
> > > On 4/9/20, 4:13 PM, "Bioc-devel on behalf of Hervé Pagès" <bioc-devel-bounces using r-project.org on behalf of hpages using fredhutch.org> wrote:
> > >
> > > Hello Bioconductor developers,
> > >
> > > As you've probably noticed already, we're building BioC 3.11 on Mac again:
> > >
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg&s=Lp71UxuNF1FLTNhqFVg1NzXogj7yQv7lckRDEXnB2AY&e=
> > >
> > > The build target now is High Sierra (used to be El Capitan), like for
> > > the official Mac built of R 4.0.0 alpha (available here
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.r-2Dproject.org_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg&s=_fEbeaymE4PlCRQ_-LNjFj4zgEXfuztnC5NgmpXZi78&e= ) and for the Mac binary packages available on
> > > CRAN. This means that the binaries we produce are only compatible with
> > > High Sierra or higher, as long as you're using the official Mac built of
> > > R 4.0.0.
> > >
> > > IMPORTANT: CRAN and Bioconductor binary packages for Mac are NOT meant
> > > to be used with an R 4.0.0 installed from source (they're likely to
> > > crash your session, typically at load time).
> > >
> > > Using BiocManager::install() with the official Mac built of R 4.0.0 will
> > > pick up binary packages from CRAN and Bioconductor 3.11. It will fall
> > > back on source packages only when the binaries are not available.
> > >
> > > Please let us know if you run into any problem with this.
> > >
> > > Cheers,
> > > H.
> > >
> > > --
> > > 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 using fredhutch.org
> > > Phone: (206) 667-5791
> > > Fax: (206) 667-1319
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg&s=hLf_-4C9O9l7tBrgMKlvaCI-gxFf4nZEpJmB1A9NFBA&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 using fredhutch.org
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
> >
> >
>
> --
> 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 using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
>
--
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 using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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