I see bin/macosx/contrib/4.0/ now (e.g.
https://cran.r-project.org/bin/macosx/contrib/4.0/). Thanks!
H.
On 4/1/20 00:37, Simon Urbanek wrote:
Hervé,
On 1/04/2020, at 6:19 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha build from
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.r-2Dproject.org_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SgN9XTf8oSzk28ZilVDsjOU2Fpf0lRzDmF8QEBnwJno&s=n2gZ5tfjXIG7SNEmqQd8-QMsUj5t6y0-r1r-qaCgd7I&e=
for the Bioconductor build system. Bioconductor packages depend on thousands of CRAN packages and one
thing that makes it hard for us and for our users to build/check Bioconductor packages at the moment is
the absence of Mac binary packages for R 4.0.0 on CRAN. Do you have an estimate of when they will
become available?
Both the packages and R are now available. I always recommend using the Mac-master
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SgN9XTf8oSzk28ZilVDsjOU2Fpf0lRzDmF8QEBnwJno&s=-zAfQSmtuRs4uqHBVFcX5ssEWKX2vsSrEqVTwxI_WuM&e=
as "mirror" since that one is most up-to-date.
Another question is where they are going to be hosted on CRAN. We need to
follow CRAN's layout for Bioconductor package repositories.
We have removed the extra layer, the package type is back to "mac.binary", so
bin/macosx/contrib is the location.
Cheers,
Simon
Thanks!
H.
On 3/31/20 21:27, Simon Urbanek wrote:
Dear Mac users,
R 4.0.0 will be using an entirely new toolchain, entirely new build system on
entirely new macOS version and hardware. Therefore I would like to ask you
kindly to test the binaries from
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=FJYxweW9WiMXbNMPpMM0bHXy020Gx9P-dHMrWmt7YzE&e=
before the release as much as you can. Raising any issues after the release is
too late! So please, please, test the pre-releases. Report any issues either
directly to me or this mailing list.
The nightly builds are signed, but not necessarily notarized. However, the
build fulfils Apple's conditions and is known to pass notarization (in fact the
the package available for download today is actually notarized) so it should be
a good test for the release which will be notarized and should work on Catalina.
For those that want to replicate our setup - technical details: we are now building with macOS 10.13
(High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and
GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13
target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it
easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are
available in
https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_libs-2D4_&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=3ZbcXBticg_8MfXltGKdQ9SFNqqeLqqwK_pUhEet7QY&e=
The new R build system is in
https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_R4&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=Mmt7_pVM5aUDR3hz93-e-PtadG7wSYpaZe8Ayi5Pv4I&e=
Packages build system has not changed and is in
https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_packages&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=eId6n08LVeIAMhMXe3jvLFKn9QGi4_by8owFreDDc84&e=
We also plan to have a mac-builder available with similar function as the
win-builder where pre-submission tests can be performed and potentially a
Travis template.
Please test R pre-releases and provide feedback!
Thanks,
Simon
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--
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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--
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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