[Bioc-devel] xps build problem on veracruz2
Hervé Pagès
hpages at fredhutch.org
Thu Apr 20 19:59:00 CEST 2017
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... 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
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