Re: [Bioc-devel] xps build problem on veracruz2
scouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interesti
Re: [Bioc-devel] xps build problem on veracruz2
enbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the sam
Re: [Bioc-devel] xps build problem on veracruz2
e=OFF ../root Then built with: cmake --build . -- -j4 Then installed with: sudo cmake --build . --target install And the libraries got installed under /usr/local/root/lib/root So when trying to install the latest xps, loading xps.so failed for me because the ROOT libraries were not found. The following change to Makefile.arch fixed the problem: $ svn diff Makefile.arch Index: Makefile.arch === --- Makefile.arch(revision 129046) +++ Makefile.arch(working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clan
Re: [Bioc-devel] xps build problem on veracruz2
ch Index: Makefile.arch === --- Makefile.arch(revision 129046) +++ Makefile.arch(working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R
Re: [Bioc-devel] xps build problem on veracruz2
who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia
Re: [Bioc-devel] xps build problem on veracruz2
On 04/22/2017 02:57 PM, cstrato wrote: Dear Herve, Thank you for your efforts to get xps running. I will make the changes in Makefile.arch, too, and update README and rename it to install. I am also surprised that the libs get installed under /lib/root, and I will check if there is a reason for this. As far as I remember, long time ago someone had a similar problem, see e.g.: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_51838_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=lvjHdGnauUA25Q4WQU1Y7Sn74tcZrxSh529Bwgg5tG4&s=P0qNlFiUPP9UB0MiGeyiKvTPduWT0c3yp24Q7hNkWDY&e= Do you use the environment variable ROOTSYS? I gave you the full transcript of what I do for configure/build/install. I'm following the "fix location" installation procedure as described here: https://root.cern.ch/building-root so no ROOTSYS (the above document doesn't even mention that variable). H. Best regards, Christian On 04/22/17 22:36, Hervé Pagès wrote: Hi Christian, Thanks for the update. Glad it works for you. One small thing is that, if CMAKE_INSTALL_PREFIX is specified when configuring ROOT, the ROOT libs get installed under /lib/root, not under /lib. I was surprised by this, but that's what I got when I installed ROOT on veracruz2. I configured with: export CC=/usr/local/clang4/bin/clang export CXX=/usr/local/clang4/bin/clang++ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/root -Dgnuinstall=ON -Dfortran=OFF -Dmysql=OFF -Dsqlite=OFF ../root Then built with: cmake --build . -- -j4 Then installed with: sudo cmake --build . --target install And the libraries got installed under /usr/local/root/lib/root So when trying to install the latest xps, loading xps.so failed for me because the ROOT libraries were not found. The following change to Makefile.arch fixed the problem: $ svn diff Makefile.arch Index: Makefile.arch === --- Makefile.arch(revision 129046) +++ Makefile.arch(working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, At the moment I found also the following link: https://www.jlab.org/theory/tag/cosyn/manual.pdf which states: Error Wrong ELF class. If you get errors mentioning ELF-class then you are probably linking 64 to 32 bit code which does not compute. Make sure you are linking to the 64 bit libraries of root and not the 32 bit ones. For me the 64 bit libraries were located in /usr/local/lib/root while the 32 bit ones were in /usr/local/root/lib/root. I am not sure what this means and if it is helpful for you. Best regards, Christian On 04/22/17 23:57, cstrato wrote: Dear Herve, Thank you for your efforts to get xps running. I will make the changes in Makefile.arch, too, and update README and rename it to install. I am also surprised that the libs get installed under /lib/root, and I will check if there is a reason for this. As far as I remember, long time ago someone had a similar problem, see e.g.: https://support.bioconductor.org/p/51838/ Do you use the environment variable ROOTSYS? Best regards, Christian On 04/22/17 22:36, Hervé Pagès wrote: Hi Christian, Thanks for the update. Glad it works for you. One small thing is that, if CMAKE_INSTALL_PREFIX is specified when configuring ROOT, the ROOT libs get installed under /lib/root, not under /lib. I was surprised by this, but that's what I got when I installed ROOT on veracruz2. I configured with: export CC=/usr/local/clang4/bin/clang export CXX=/usr/local/clang4/bin/clang++ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/root -Dgnuinstall=ON -Dfortran=OFF -Dmysql=OFF -Dsqlite=OFF ../root Then built with: cmake --build . -- -j4 Then installed with: sudo cmake --build . --target install And the libraries got installed under /usr/local/root/lib/root So when trying to install the latest xps, loading xps.so failed for me because the ROOT libraries were not found. The following change to Makefile.arch fixed the problem: $ svn diff Makefile.arch Index: Makefile.arch === --- Makefile.arch(revision 129046) +++ Makefile.arch(working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, Thank you for your efforts to get xps running. I will make the changes in Makefile.arch, too, and update README and rename it to install. I am also surprised that the libs get installed under /lib/root, and I will check if there is a reason for this. As far as I remember, long time ago someone had a similar problem, see e.g.: https://support.bioconductor.org/p/51838/ Do you use the environment variable ROOTSYS? Best regards, Christian On 04/22/17 22:36, Hervé Pagès wrote: Hi Christian, Thanks for the update. Glad it works for you. One small thing is that, if CMAKE_INSTALL_PREFIX is specified when configuring ROOT, the ROOT libs get installed under /lib/root, not under /lib. I was surprised by this, but that's what I got when I installed ROOT on veracruz2. I configured with: export CC=/usr/local/clang4/bin/clang export CXX=/usr/local/clang4/bin/clang++ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/root -Dgnuinstall=ON -Dfortran=OFF -Dmysql=OFF -Dsqlite=OFF ../root Then built with: cmake --build . -- -j4 Then installed with: sudo cmake --build . --target install And the libraries got installed under /usr/local/root/lib/root So when trying to install the latest xps, loading xps.so failed for me because the ROOT libraries were not found. The following change to Makefile.arch fixed the problem: $ svn diff Makefile.arch Index: Makefile.arch === --- Makefile.arch(revision 129046) +++ Makefile.arch(working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_Zf
Re: [Bioc-devel] xps build problem on veracruz2
Hi Christian, Thanks for the update. Glad it works for you. One small thing is that, if CMAKE_INSTALL_PREFIX is specified when configuring ROOT, the ROOT libs get installed under /lib/root, not under /lib. I was surprised by this, but that's what I got when I installed ROOT on veracruz2. I configured with: export CC=/usr/local/clang4/bin/clang export CXX=/usr/local/clang4/bin/clang++ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/root -Dgnuinstall=ON -Dfortran=OFF -Dmysql=OFF -Dsqlite=OFF ../root Then built with: cmake --build . -- -j4 Then installed with: sudo cmake --build . --target install And the libraries got installed under /usr/local/root/lib/root So when trying to install the latest xps, loading xps.so failed for me because the ROOT libraries were not found. The following change to Makefile.arch fixed the problem: $ svn diff Makefile.arch Index: Makefile.arch === --- Makefile.arch (revision 129046) +++ Makefile.arch (working copy) @@ -261,7 +261,7 @@ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD= $(MACOSXTARGET) g++ #LDFLAGS = $(OPT2) -LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib +LDFLAGS = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root UNDEFOPT = dynamic_lookup # The SOFLAGS will be used to create the .dylib, # the .so will be created separately Also note that the rpaths specified at linking time get hardcoded in xps.so: veracruz2:src biocbuild$ otool -l xps.so | tail -n 18 Load command 31 cmd LC_RPATH cmdsize 32 path /usr/local/root/lib (offset 12) Load command 32 cmd LC_RPATH cmdsize 40 path /usr/local/root/lib/root (offset 12) Load command 33 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 4141784 datasize 14336 Load command 34 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 4156120 datasize 904 So the end user will need to have the ROOT libraries at these locations too (unless s/he installs from source of course). This would need to be explained in xps README file (which BTW should preferably be named INSTALL). Thanks, H. On 04/22/2017 05:15 AM, cstrato wrote: Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of R
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, I am glad to inform you that I have just uploaded version xps_1.35.3 to BioC-dev branch. I have followed your suggestion to use -rpath and have eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH. I have tested the new version on both Yosemite and on Sierra with csrutil enabled! Thus I assume that it will also run on El Capitan. Best regards, Christian P.S.: Please allow me to comment on your note on [DY]LD_LIBRARY_PATH. As you know xps was uploaded to Bioc 10 years ago (with your kind help) and is available on BioC since 9 years. At that time the environment variables [DY]LD_LIBRARY_PATH were necessary, and for many years required by ROOT. Since xps did run on the Mac on all systems from Leopard till Yosemite w/o problems I had no need to change it. Furthermore, I had not heard that the use of these variables have been discouraged, just like many other developers who only now realize that they have to use rpath or simply disable csrutil (I have realized this when googling around). On 04/21/17 00:29, Hervé Pagès wrote: Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of
Re: [Bioc-devel] xps build problem on veracruz2
Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - > From: "Hervé Pagès" > To: "cstrato" , "Dan Tenenbaum" > Cc: "bioc-devel" > Sent: Thursday, April 20, 2017 3:17:23 PM > Subject: Re: [Bioc-devel] xps build problem on veracruz2 > On 04/20/2017 03:01 PM, cstrato wrote: >> Dear Herve, >> >> Doing 'csrutil disable' does indeed solve the problem, since: >> >> 1, in this way I was able to build xps on Mac OS Sierra >> >> 2, in this way I could already help one user of xps, see: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= >> >> This means, that users of xps seem to be willing to disable csrutil. > > I'm not a statistician but I wouldn't draw conclusions from a sample > of size 1. Mac users who cannot install xps on their machine will > use something else, or, if they desperately need xps, they will > grab a Linux box. > > Sorry but disabling SIP on our Mac builders is not an option. > >> >> >> >> However, I just realized that there may be an even greater problem, >> namely, which version of ROOT should a user install? >> >> People can download ROOT binaries built with XCode 7.x from: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= >> for OS X 10.10 and 10.11. >> >> Thus for El Capitan they can download the following binaries: >> - root_v5.34.36.macosx64-10.11-clang70.dmg >> - root_v5.34.36.macosx64-10.11-clang70.tar.gz >> >> Did you install one of those binaries or did you compile ROOT from source? > > As I said earlier, I compiled ROOT 5 from source on veracruz2. > >> >> With the help of my README file people could compile ROOT from source >> for XCode 8.x. >> >> >> However, you have mentioned that the CRAN people are using clang 4.0.0 >> for producing the Mac binaries of R and CRAN packages and thus you are >> using the same on veracruz2. > > Yes. > >> >> Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which >> is not officially supported by Apple? > > With clang 4.0.0. > >> >> The question is whether xps built with this version of ROOT will work >> with the ROOT binaries which people can download from ROOT? > > I guess someone will need to figure this out. > > Note that if people need to compile their own ROOT anyway in order to > be able to use the xps binary we distribute, then they should also be > able to install xps from source. So that defeats the purpose of > providing a binary in the first place. > > Cheers, > H. > >> >> Best regards, >> Christian >> >> >> >> On 04/20/17 20:00, Hervé Pagès wrote: >>> On 04/20/2017 10:59 AM, Hervé Pagès wrote: >>>> Hi Christian, >>>> >>>> Disabling 'csrutil disable' might help xps on veracruz2 but that >>> ^^ >>> oops, no double negative intended here. I meant, doing 'csrutil disable' >>> might help... etc >>> >>> H. >>> >>>> won't help your end users. >>>> >>>> I'm no expert in developing a package on Mac but other people on >>>> this list are. Also R-SIG-Mac might be a good place to seek help >>>> for this. >>>> >>>> Cheers, >>>> H. >>>> >>>> >>>> On 04/20/2017 10:53 AM, cstrato wrote: >>>>> Dear Herve, >>>>> >>>>> Thank you for your efforts to try to install xps. I am glad to hear >>>>> that >>>>> you could build ROOT 5 from source. >>>>> >>>>> It's a pity that Apple does no longer allow the use of >>>>> DYLD_LIBRARY_PATH. This seems to break the code of a lot of people >>>>> (when >>>>> googling around). >>>>> >>>>> I will try to change the build process and will see if I succeed. >>>>> However, at the moment I
Re: [Bioc-devel] xps build problem on veracruz2
Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - From: "Hervé Pagès" To: "cstrato" , "Dan Tenenbaum" Cc: "bioc-devel" Sent: Thursday, April 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoK
Re: [Bioc-devel] xps build problem on veracruz2
On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to disable csrutil. I'm not a statistician but I wouldn't draw conclusions from a sample of size 1. Mac users who cannot install xps on their machine will use something else, or, if they desperately need xps, they will grab a Linux box. Sorry but disabling SIP on our Mac builders is not an option. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg&s=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc&e= for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? As I said earlier, I compiled ROOT 5 from source on veracruz2. With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Yes. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? With clang 4.0.0. The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? I guess someone will need to figure this out. Note that if people need to compile their own ROOT anyway in order to be able to use the xps binary we distribute, then they should also be able to install xps from source. So that defeats the purpose of providing a binary in the first place. Cheers, H. Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the same effect.' Do you think that using LD_RUN_PATH would solve the problem? If yes, then how? 4, Googling for the DYLD_LIBRARY_PATH problem I have also found the following discussion: https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk&e= There, one answ
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://support.bioconductor.org/p/90056/#90247 This means, that users of xps seem to be willing to disable csrutil. However, I just realized that there may be an even greater problem, namely, which version of ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https://root.cern.ch/content/release-53436 for OS X 10.10 and 10.11. Thus for El Capitan they can download the following binaries: - root_v5.34.36.macosx64-10.11-clang70.dmg - root_v5.34.36.macosx64-10.11-clang70.tar.gz Did you install one of those binaries or did you compile ROOT from source? With the help of my README file people could compile ROOT from source for XCode 8.x. However, you have mentioned that the CRAN people are using clang 4.0.0 for producing the Mac binaries of R and CRAN packages and thus you are using the same on veracruz2. Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which is not officially supported by Apple? The question is whether xps built with this version of ROOT will work with the ROOT binaries which people can download from ROOT? Best regards, Christian On 04/20/17 20:00, Hervé Pagès wrote: On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the same effect.' Do you think that using LD_RUN_PATH would solve the problem? If yes, then how? 4, Googling for the DYLD_LIBRARY_PATH problem I have also found the following discussion: https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk&e= There, one answer mentioned: 'Also, rpath is a good idea. Also see install_name_tool, which can change the load paths of libraries.' Doing a search for 'install_name_tool' I found: https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E&e= There, one answer mentioned (see also $man install_name_tool): 'Having experimented more: install_name_tool -id newname file will do the trick.' See also: https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo&e= Do you think that either using the environment variable LD_RUN_PATH or using 'install_name_tool' could solve the problem without having to use '-rpath'? Thank you in advance. Best regards, Christian On 04/19/17 22:51, Hervé Pagès
Re: [Bioc-devel] xps build problem on veracruz2
On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the same effect.' Do you think that using LD_RUN_PATH would solve the problem? If yes, then how? 4, Googling for the DYLD_LIBRARY_PATH problem I have also found the following discussion: https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk&e= There, one answer mentioned: 'Also, rpath is a good idea. Also see install_name_tool, which can change the load paths of libraries.' Doing a search for 'install_name_tool' I found: https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E&e= There, one answer mentioned (see also $man install_name_tool): 'Having experimented more: install_name_tool -id newname file will do the trick.' See also: https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo&e= Do you think that either using the environment variable LD_RUN_PATH or using 'install_name_tool' could solve the problem without having to use '-rpath'? Thank you in advance. Best regards, Christian On 04/19/17 22:51, Hervé Pagès wrote: Hi Christian, So I installed ROOT 5 from source on veracruz2. It's in /usr/local/root. However, Apple's SIP (System Integrity Protection, new and enabled by default on El Capitan) is getting in the way when trying to install xps. That's because xps configure and build process relies on DYLD_LIBRARY_PATH. Problem is that this environment variable (and any other variables that control dynamic loading) is not inherited by child processes when SIP is on: veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi yep! veracruz2:~ biocbuild$ sh sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi nope! That breaks xps configure script: veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH /usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib veracruz2:~ biocbuild$ R CMD INSTALL xps * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘xps’ ... checking for gcc... clang checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we ar
Re: [Bioc-devel] xps build problem on veracruz2
Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato wrote: Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM&e= Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the same effect.' Do you think that using LD_RUN_PATH would solve the problem? If yes, then how? 4, Googling for the DYLD_LIBRARY_PATH problem I have also found the following discussion: https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk&e= There, one answer mentioned: 'Also, rpath is a good idea. Also see install_name_tool, which can change the load paths of libraries.' Doing a search for 'install_name_tool' I found: https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E&e= There, one answer mentioned (see also $man install_name_tool): 'Having experimented more: install_name_tool -id newname file will do the trick.' See also: https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo&e= Do you think that either using the environment variable LD_RUN_PATH or using 'install_name_tool' could solve the problem without having to use '-rpath'? Thank you in advance. Best regards, Christian On 04/19/17 22:51, Hervé Pagès wrote: Hi Christian, So I installed ROOT 5 from source on veracruz2. It's in /usr/local/root. However, Apple's SIP (System Integrity Protection, new and enabled by default on El Capitan) is getting in the way when trying to install xps. That's because xps configure and build process relies on DYLD_LIBRARY_PATH. Problem is that this environment variable (and any other variables that control dynamic loading) is not inherited by child processes when SIP is on: veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi yep! veracruz2:~ biocbuild$ sh sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi nope! That breaks xps configure script: veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH /usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib veracruz2:~ biocbuild$ R CMD INSTALL xps * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘xps’ ... checking for gcc... clang checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang accepts -g... yes checking for clang option to accept ANSI C... none needed checking how to run the C preprocessor... c
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, Thank you for your efforts to try to install xps. I am glad to hear that you could build ROOT 5 from source. It's a pity that Apple does no longer allow the use of DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when googling around). I will try to change the build process and will see if I succeed. However, at the moment I have a couple of questions: 1, Is there any reason that you do not want to 'csrutil disable'? 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my 'configure.in' file, however, I have also to change the 'Makefile'. Since you say that the problem can be solved by adding the -rpath flag when linking, I assume that I have to change the following line in my 'Makefile': $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) Since I am not familiar with -rpath can you give me a hint how to change it? 3, There is a Wikipedia explanation for '-rpath', see: https://en.wikipedia.org/wiki/Rpath Interestingly, there is the following line: 'Instead of specifying the -rpath to the linker, the environment variable LD_RUN_PATH can be set to the same effect.' Do you think that using LD_RUN_PATH would solve the problem? If yes, then how? 4, Googling for the DYLD_LIBRARY_PATH problem I have also found the following discussion: https://forums.macrumors.com/threads/is-it-ok-to-use-dyld_library_path-on-mac-os-x-and-what%C2%92s-the-dynamic-library-search.956258/ There, one answer mentioned: 'Also, rpath is a good idea. Also see install_name_tool, which can change the load paths of libraries.' Doing a search for 'install_name_tool' I found: http://stackoverflow.com/questions/2985315/using-install-name-tool-whats-going-wrong There, one answer mentioned (see also $man install_name_tool): 'Having experimented more: install_name_tool -id newname file will do the trick.' See also: http://qin.laya.com/tech_coding_help/dylib_linking.html Do you think that either using the environment variable LD_RUN_PATH or using 'install_name_tool' could solve the problem without having to use '-rpath'? Thank you in advance. Best regards, Christian On 04/19/17 22:51, Hervé Pagès wrote: Hi Christian, So I installed ROOT 5 from source on veracruz2. It's in /usr/local/root. However, Apple's SIP (System Integrity Protection, new and enabled by default on El Capitan) is getting in the way when trying to install xps. That's because xps configure and build process relies on DYLD_LIBRARY_PATH. Problem is that this environment variable (and any other variables that control dynamic loading) is not inherited by child processes when SIP is on: veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi yep! veracruz2:~ biocbuild$ sh sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo 'nope!'; fi nope! That breaks xps configure script: veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH /usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib veracruz2:~ biocbuild$ R CMD INSTALL xps * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘xps’ ... checking for gcc... clang checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang accepts -g... yes checking for clang option to accept ANSI C... none needed checking how to run the C preprocessor... clang -E checking for gcc... (cached) clang checking whether we are using the GNU C compiler... (cached) yes checking whether clang accepts -g... (cached) yes checking for clang option to accept ANSI C... (cached) none needed found ROOT version 5.34/36 in directory /usr/local/root xps configuration error: You must set the shell variable LD_LIBRARY_PATH to the directory where ROOT resides and re-run R CMD INSTALL e.g., (using Bourne shell syntax): export "LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH" R CMD INSTALL xps Please consult the README file for more information ERROR: configuration failed for package ‘xps’ * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/xps’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/xps’ That also breaks the dynlib mechanism because, after I managed to produce xps.so, it turns out that this shared object is linked to the ROOT libraries via the @rpath mechanism: veracruz2:src biocbuild$ otool -L xps.so xps.so: xps.so (compatibility version 0.0.0, current version 0.0.0) @rpath/libGui.so (compatibility version 0.0.0, current version 0.0.0) @rpath/lib
Re: [Bioc-devel] xps build problem on veracruz2
g: -rpath $(shell $(ROOTCONFIG) --prefix)/lib Do you think you can revisit xps configure and build process? Make sure you test it on a machine where SIP is enabled. Thanks, H. On 03/24/2017 12:14 PM, cstrato wrote: On 03/24/17 19:55, Hervé Pagès wrote: On 03/24/2017 11:37 AM, cstrato wrote: On 03/24/17 19:23, Hervé Pagès wrote: On 03/24/2017 11:10 AM, cstrato wrote: On 03/24/17 18:02, Hervé Pagès 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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 u
Re: [Bioc-devel] xps build problem on veracruz2
On 03/24/17 19:55, Hervé Pagès wrote: On 03/24/2017 11:37 AM, cstrato wrote: On 03/24/17 19:23, Hervé Pagès wrote: On 03/24/2017 11:10 AM, cstrato wrote: On 03/24/17 18:02, Hervé Pagès 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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 w
Re: [Bioc-devel] xps build problem on veracruz2
On 03/24/2017 11:37 AM, cstrato wrote: On 03/24/17 19:23, Hervé Pagès wrote: On 03/24/2017 11:10 AM, cstrato wrote: On 03/24/17 18:02, Hervé Pagès 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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 new
Re: [Bioc-devel] xps build problem on veracruz2
On 03/24/17 19:23, Hervé Pagès wrote: On 03/24/2017 11:10 AM, cstrato wrote: On 03/24/17 18:02, Hervé Pagès 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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, Hervé Pagès 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 wrot
Re: [Bioc-devel] xps build problem on veracruz2
On 03/24/2017 11:10 AM, cstrato wrote: On 03/24/17 18:02, Hervé Pagès 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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, Hervé Pagès 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 vera
Re: [Bioc-devel] xps build problem on veracruz2
On 03/24/17 18:02, Hervé Pagès 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://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? 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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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, Hervé Pagès 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_wJYbW0WYiZvSXAJJKaaPh
Re: [Bioc-devel] xps build problem on veracruz2
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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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, Hervé Pagès 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@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= -- Hervé Pagès Program in Comput
Re: [Bioc-devel] xps build problem on veracruz2
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: "Hervé Pagès" To: "cstrato" , "bioc-devel" 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, Hervé Pagès 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@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= -- 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
- Original Message - > From: "Hervé Pagès" > To: "cstrato" , "bioc-devel" > 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, Hervé Pagès 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@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= >>>> >>>> >>>> >>> > > -- > 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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. Cheers, H. Best regards, Christian On 03/23/17 17:47, Hervé Pagès 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@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= -- 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] xps build problem on veracruz2
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, Hervé Pagès 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@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= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
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@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= -- 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] xps build problem on veracruz2
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 > _._._._._._._._._._._._._._._._._._ > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel