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-boun...@r-project.org on behalf of hpa...@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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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