[Bioc-devel] New Mac builder and availability of Mac binary packages

[Hervé Pagès]

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