Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://root.cern.ch/download/root_v5.34.36.source.tar.gz The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
[Bioc-devel] xps build problem on veracruz2
13 messages · cstrato, Obenchain, Valerie, Dan Tenenbaum +1 more
Hi, veracruz2 is in testing / setup stage and is not the official Mac devel builder. See my post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010629.html Currently there are more pressing issues than the ROOT system dependency. Rest assured that ROOT will be correctly installed on veracruz2 when it becomes the official builder, as it was on toluca2 when that machine replaced oaxaca. Valerie
On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://root.cern.ch/download/root_v5.34.36.source.tar.gz The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H.
On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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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
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5. BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.) Best regards, Christian
On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that. Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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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
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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-- 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
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R/Bioc is still building on Mavericks, and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc. However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow. But I understand that this is a decision the CRAN people have to make. Best regards, Christian
On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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-- 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
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On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago: https://r.research.att.com/
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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-- 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&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
On 03/24/17 18:02, Herv? Pag?s wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago:
You are right, I did not check R devel.
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
You probably misunderstood what I wanted to say. It is clear to me that you are doing a great job distributing thousands of package binaries. No one does know it better than me with the special problems you have to build binaries for xps. I really appreciate that during all these years you and Dan (and others) managed to support xps like all other BioC packages. I meant that from the user standpoint it probably does not matter much which of these three systems are used to build BioC, in contrast to Sierra. But as you said below backward-compatibility is always lost, so the question which system to use to build R/BioC is always tricky. Maybe, the best (?) decision would be to use the system which most Mac users are currently using, but I don't know. Best regards, Christian
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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-- 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Herv? Pag?s wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago:
You are right, I did not check R devel.
https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
You probably misunderstood what I wanted to say. It is clear to me that you are doing a great job distributing thousands of package binaries. No one does know it better than me with the special problems you have to build binaries for xps. I really appreciate that during all these years you and Dan (and others) managed to support xps like all other BioC packages. I meant that from the user standpoint it probably does not matter much which of these three systems are used to build BioC, in contrast to Sierra.
Of course it matters. If you use an older OS than the one we use to produce the binaries then some binaries won't work for you. You keep missing the whole point. H.
But as you said below backward-compatibility is always lost, so the question which system to use to build R/BioC is always tricky. Maybe, the best (?) decision would be to use the system which most Mac users are currently using, but I don't know. Best regards, Christian
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
_______________________________________________ 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=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&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 at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&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
On 03/24/17 19:23, Herv? Pag?s wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Herv? Pag?s wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago:
You are right, I did not check R devel.
https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
You probably misunderstood what I wanted to say. It is clear to me that you are doing a great job distributing thousands of package binaries. No one does know it better than me with the special problems you have to build binaries for xps. I really appreciate that during all these years you and Dan (and others) managed to support xps like all other BioC packages. I meant that from the user standpoint it probably does not matter much which of these three systems are used to build BioC, in contrast to Sierra.
Of course it matters. If you use an older OS than the one we use to produce the binaries then some binaries won't work for you. You keep missing the whole point. H.
Sorry, but I do understand this point. Users who are still using e.g. Snow Leopard (because they think this was the best system) will have problems. For that reason I thought that maybe it is best to use the system which is currently used by most users. Christian
But as you said below backward-compatibility is always lost, so the question which system to use to build R/BioC is always tricky. Maybe, the best (?) decision would be to use the system which most Mac users are currently using, but I don't know. Best regards, Christian
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
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-- 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=
On 03/24/2017 11:37 AM, cstrato wrote:
On 03/24/17 19:23, Herv? Pag?s wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Herv? Pag?s wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago:
You are right, I did not check R devel.
https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
You probably misunderstood what I wanted to say. It is clear to me that you are doing a great job distributing thousands of package binaries. No one does know it better than me with the special problems you have to build binaries for xps. I really appreciate that during all these years you and Dan (and others) managed to support xps like all other BioC packages. I meant that from the user standpoint it probably does not matter much which of these three systems are used to build BioC, in contrast to Sierra.
Of course it matters. If you use an older OS than the one we use to produce the binaries then some binaries won't work for you. You keep missing the whole point. H.
Sorry, but I do understand this point. Users who are still using e.g. Snow Leopard (because they think this was the best system) will have problems. For that reason I thought that maybe it is best to use the system which is currently used by most users.
That would be the thing to do if we didn't have neither forward- nor backward- compatibility. But we *do* have forward-compatibility. So there is no reason to use the system which is currently used by most users. It's enough to make sure that we use a system that is *compatible* with what most users have. And also not too old because it's hard to find powerful hardware that runs old OS X versions and because many software components needed for the builds are not available or not maintained anymore for old OS X versions. Like Dan said, it's a tradeoff. H.
Christian
But as you said below backward-compatibility is always lost, so the question which system to use to build R/BioC is always tricky. Maybe, the best (?) decision would be to use the system which most Mac users are currently using, but I don't know. Best regards, Christian
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
_______________________________________________ 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=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&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 at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&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
On 03/24/17 19:55, Herv? Pag?s wrote:
On 03/24/2017 11:37 AM, cstrato wrote:
On 03/24/17 19:23, Herv? Pag?s wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Herv? Pag?s wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few days ago:
You are right, I did not check R devel.
https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
and before was built on Snow Leopard (which many people are sill using). Personally I think that it does not make much difference whether Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
How much experience you have with setting a Mavericks or El Capitan build machine to build and distribute thousands of package binaries for hundreds ot thousands of users?
You probably misunderstood what I wanted to say. It is clear to me that you are doing a great job distributing thousands of package binaries. No one does know it better than me with the special problems you have to build binaries for xps. I really appreciate that during all these years you and Dan (and others) managed to support xps like all other BioC packages. I meant that from the user standpoint it probably does not matter much which of these three systems are used to build BioC, in contrast to Sierra.
Of course it matters. If you use an older OS than the one we use to produce the binaries then some binaries won't work for you. You keep missing the whole point. H.
Sorry, but I do understand this point. Users who are still using e.g. Snow Leopard (because they think this was the best system) will have problems. For that reason I thought that maybe it is best to use the system which is currently used by most users.
That would be the thing to do if we didn't have neither forward- nor backward- compatibility. But we *do* have forward-compatibility. So there is no reason to use the system which is currently used by most users. It's enough to make sure that we use a system that is *compatible* with what most users have. And also not too old because it's hard to find powerful hardware that runs old OS X versions and because many software components needed for the builds are not available or not maintained anymore for old OS X versions. Like Dan said, it's a tradeoff. H.
You are right, using a system which is compatible with what most users have, is the best choice. Christian
Christian
But as you said below backward-compatibility is always lost, so the question which system to use to build R/BioC is always tricky. Maybe, the best (?) decision would be to use the system which most Mac users are currently using, but I don't know. Best regards, Christian
However, Sierra is different, and when the CRAN people are experimenting with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, then backwards-compatibility would probably be lost anyhow.
I think you misunderstood what Dan said. Backward-compatibility is always lost i.e. binaries built on a given OS X versions are not guaranteed to be backward compatible with older OS X versions. That's why building them on the latest OS X version is a bad idea.
But I understand that this is a decision the CRAN people have to make.
You're welcome to discuss this choice on the R-SIG-Mac mailing list. Cheers, H.
Best regards, Christian On 03/24/17 01:10, Dan Tenenbaum wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org> Sent: Thursday, March 23, 2017 12:14:38 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5.
OK
BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.)
Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that.
Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan
Cheers, H.
Best regards, Christian On 03/23/17 17:47, Herv? Pag?s wrote:
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
_______________________________________________ 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=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&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 at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=