[Bioc-devel] New Mac builder and availability of Mac binary packages
hp@ge@ @end|ng |rom |redhutch@org
Fri Apr 10 19:31:28 CEST 2020
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
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.
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?
> 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:
> 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.
> 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
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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