[Bioc-devel] xps build problem on veracruz2
Hervé Pagès
hpages at fredhutch.org
Sat Apr 22 22:36:27 CEST 2017
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
<prefix>/lib/root, not under <prefix>/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" <hpages at fredhutch.org>
>>>> To: "cstrato" <cstrato at aon.at>, "Dan Tenenbaum"
>>>> <dtenenba at fredhutch.org>
>>>> Cc: "bioc-devel" <bioc-devel at r-project.org>
>>>> 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 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... 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/libCore.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libCint.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libRIO.so (compatibility version 0.0.0, current version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libNet.so (compatibility version 0.0.0, current version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libHist.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libGraf.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libGraf3d.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libGpad.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libTree.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libRint.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libPostscript.so (compatibility version 0.0.0, current
>>>>>>>>> version 0.0.0)
>>>>>>>>> @rpath/libMatrix.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libPhysics.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libMathCore.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libThread.so (compatibility version 0.0.0, current
>>>>>>>>> version
>>>>>>>>> 0.0.0)
>>>>>>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
>>>>>>>>> current
>>>>>>>>> version 1226.10.1)
>>>>>>>>> @rpath/libGed.so (compatibility version 0.0.0, current version
>>>>>>>>> 0.0.0)
>>>>>>>>> @rpath/libTreePlayer.so (compatibility version 0.0.0, current
>>>>>>>>> version 0.0.0)
>>>>>>>>> @rpath/libTreeViewer.so (compatibility version 0.0.0, current
>>>>>>>>> version 0.0.0)
>>>>>>>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current
>>>>>>>>> version 120.1.0)
>>>>>>>>>
>>>>>>>>> so it can't be loaded in R:
>>>>>>>>>
>>>>>>>>>> dyn.load("xps.so")
>>>>>>>>> Error in dyn.load("xps.so") :
>>>>>>>>> unable to load shared object
>>>>>>>>> '/Users/biocbuild/bbs-3.5-bioc/xps/src/xps.so':
>>>>>>>>> dlopen(/Users/biocbuild/bbs-3.5-bioc/xps/src/xps.so, 6):
>>>>>>>>> Library not
>>>>>>>>> loaded: @rpath/libGui.so
>>>>>>>>> Referenced from: /Users/biocbuild/bbs-3.5-bioc/xps/src/xps.so
>>>>>>>>> Reason: image not found
>>>>>>>>>
>>>>>>>>> because R has no access to DYLD_LIBRARY_PATH:
>>>>>>>>>
>>>>>>>>>> Sys.getenv("DYLD_LIBRARY_PATH")
>>>>>>>>> [1] ""
>>>>>>>>>
>>>>>>>>> This can be addressed by adding the following flag when linking:
>>>>>>>>>
>>>>>>>>> -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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>>>> snip >>>
>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 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 at r-project.org mailing list
>>>>>>>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e=
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>> 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: hpages at fredhutch.org
>>>>>>>>>>>>>>>>>> Phone: (206) 667-5791
>>>>>>>>>>>>>>>>>> Fax: (206) 667-1319
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>> --
>>>> 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: hpages at fredhutch.org
>>>> Phone: (206) 667-5791
>>>> Fax: (206) 667-1319
>>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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