[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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