Re: [Bioc-devel] New Mac builder and availability of Mac binary packages
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" 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" 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" 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=Lp71UxuNF1FLTNhqFVg1NzXogj7yQv7lckRDEXnB2AY= > > > > 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=_fEbeaymE4PlCRQ_-LNjFj4zgEXfuztnC5NgmpXZi78= ) 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 > >
Re: [Bioc-devel] New Mac builder and availability of Mac binary packages
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" 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" 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=Lp71UxuNF1FLTNhqFVg1NzXogj7yQv7lckRDEXnB2AY= > > 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=_fEbeaymE4PlCRQ_-LNjFj4zgEXfuztnC5NgmpXZi78= ) 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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=hLf_-4C9O9l7tBrgMKlvaCI-gxFf4nZEpJmB1A9NFBA= > > > -- 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 -- 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://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] New Mac builder and availability of Mac binary packages
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" 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=Lp71UxuNF1FLTNhqFVg1NzXogj7yQv7lckRDEXnB2AY= 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=_fEbeaymE4PlCRQ_-LNjFj4zgEXfuztnC5NgmpXZi78= ) 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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EBz1PFzIr1V4NU9MH7hPVYFFnKmMa1I6Vc8I9gjbOSg=hLf_-4C9O9l7tBrgMKlvaCI-gxFf4nZEpJmB1A9NFBA= -- 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://stat.ethz.ch/mailman/listinfo/bioc-devel
