[Bioc-devel] xps build problem on veracruz2
Hervé Pagès
hpages at fredhutch.org
Sun Apr 23 02:32:47 CEST 2017
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 <prefix>/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
>> <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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