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

Fri, Apr 10, 2020 10:31 AM

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 Herv? Pag?s" <bioc-devel-bounces at r-project.org on behalf of hpages at 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.
     
     --
     Herv? Pag?s
     
     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 at fredhutch.org
     Phone:  (206) 667-5791
     Fax:    (206) 667-1319

     _______________________________________________
     Bioc-devel at 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=

Herv? Pag?s

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 at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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

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