Re: [Bioc-devel] xps build problem on veracruz2
On 04/22/2017 03:06 PM, cstrato wrote: Dear Herve, At the moment I found also the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jlab.org_theory_tag_cosyn_manual.pdf&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7tn_6rjQ1Z2nt6iYVeE8untsO9LEqi2ckK_BvP73l2s&s=Ui9eBMvQBWYFJYpwM5Jjrn_3Hjb6spCYMlb0BbdERhs&e= 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. I'm not sure how this is relevant to xps/ROOT on El Capitan. El Capitan is a 64-bit only OS (i.e. x86_64). Apple dropped the 32-bit arch (i386) years ago. H. 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://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_51838_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7tn_6rjQ1Z2nt6iYVeE8untsO9LEqi2ckK_BvP73l2s&s=31gB3jOjHIBy36ASjb9hE-_OU7g_zJtAFZOwYYrU9EY&e= 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 disab
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 PM Subject: Re: [Bioc-devel] xps build problem on veracruz2 On 04/20/2017 03:01 PM, cstrato wro
Re: [Bioc-devel] Vignette update after change in git mirror repo
Thank you, Sean and James! I think this fixed the problem, Sean - will know when the build is finished today. MUCH appreciated. On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis wrote: > Sorry I lead you astray, earlier, Maia. > > In general, you do not need to install the package in the vignette. The > first code block in the vignette where you did "eval=FALSE" is the way to > go. The second code block where you actually do the installation is > unnecessary. The package is installed by R in order to build the vignette. > > Sean > > [[alternative HTML version deleted]] ___ 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, 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 20, 2017 3:17:23 PM Subject: Re: [Bioc-devel] xps bu
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_ZfxKtn-FSJgkxMW1ZBYK1Vs&e= This means, that users of xps seem to be willing to
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 ROOT should a user install? People can download ROOT binaries built with XCode 7.x from: https:/
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 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 succ
Re: [Bioc-devel] test coverage of a shiny app
Hi Sam, This is a pertinent issue to shiny app development and there are continuing efforts to create unit tests for shiny applications. At the moment, there is a package dedicated to providing tests for shiny applications but it has not been published. See: https://github.com/rstudio/shinytest This link may also provide some testing examples: https://cran.r-project.org/web/packages/RSelenium/vignettes/shinytesting.html In the meantime, I would advise to simply test the functions and manipulations that generate the data for your shiny application. I'm eager to hear other developer's inputs on this subject. Best regards, Marcel On Tue, Apr 11, 2017 at 2:46 AM Samuel Wieczorek wrote: > Hi > > I am the developer of the packages Prostar ad DAPAR and I would like to > write some unit test for Prostar which contains a Shiny application. I > wrote a test script in the 'test' directory where I am using functions > from the shiytest package but I don't know how to really test my app > (Prostar()). And then, the result of packages_coverage is still equal to > 0%. > > Is there anyone who has already developed a Shiny app with unit tests ? > I would appreciate some examples. > > > Thanks in advance > > > Sam > > > -- > *Samuel Wieczorek > > Etude de la Dynamique des Protéomes (EDyP)* > *Laboratoire Biologie à Grande Echelle (BGE)* > *U1038 INSERM / CEA / UGA* > *Biosciences and Biotechnology Institute of Grenoble (BIG)* > *CEA / Grenoble* > *17 avenue des Martyrs* > *F-38054 Grenoble Cedex 9* > */Tél. : 04.38.78.44.14/* > */Fax : 04.38.78.50.51/* > > http://www.edyp.fr/ > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
