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Question: Installing lpsymphony on Mac OS X
0
gravatar for tohsumi
20 days ago by
tohsumi0
tohsumi0 wrote:

Greetings, I would like to install lpsymphony on my Mac running Mojave.   It compiles most of the way through, but dies when ld encounters the unknown flag -T.   This is because GNU binutils does not provide ld on Mac OS X.   I'm happy to download the source and modify it, but could someone give me a pointer on what I should change so it works with the built-in ld?   I have included below the output of ld -v as well as the error message.   Any information would be much appreciated.   Many thanks!

----

Output of ld -v below:

@(#)PROGRAM:ld  PROJECT:ld64-409.12
BUILD 17:47:51 Sep 25 2018
configured to support archs: armv6 armv7 armv7s arm64 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em
LTO support using: LLVM version 10.0.0, (clang-1000.10.44.4) (static support for 21, runtime is 21)
TAPI support using: Apple TAPI version 10.0.0 (tapi-1000.10.8)

----

Error message:

/usr/local/opt/llvm/bin/clang++ -w -g -O2 -DSYMPHONY_BUILD -TP -o symphony symphony-main.o -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -Wl,-bind_at_load  -L/usr/local/opt/openssl/lib -L/usr/local/opt/libxml2/lib -L/usr/local/opt/libxslt/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/v8@3.15/lib -L/usr/local/opt/llvm/lib -L/usr/local/opt/zlib/lib -L/usr/local/opt/sqlite/lib ./.libs/libSym.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/Cgl/src/.libs/libCgl.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/Clp/src/OsiClp/.libs/libOsiClp.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/Clp/src/.libs/libClpSolver.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/Clp/src/.libs/libClp.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/Osi/src/Osi/.libs/libOsi.a /private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmptXhVIP/R.INSTALL2afb8b8249c/lpsymphony/src/SYMPHONY/CoinUtils/src/.libs/libCoinUtils.a

ld: unknown option: -T

clang-7: error: linker command failed with exit code 1 (use -v to see invocation)

make[3]: *** [symphony] Error 1

make[2]: *** [all-recursive] Error 1

make[1]: *** [all-recursive] Error 1

make: *** [SYMPHONY.ts] Error 2

ERROR: compilation failed for package ‘lpsymphony’

* removing ‘/Users/tohsumi/Library/R/3.x/library/lpsymphony’

 

The downloaded source packages are in

‘/private/var/folders/jp/_tg6j6zj06x1ccfb1wn_7w380000gn/T/RtmpKiPNVo/downloaded_packages’

Warning message:

In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘lpsymphony’ had non-zero exit status

 

ADD COMMENTlink modified 16 days ago by Wolfgang Huber13k • written 20 days ago by tohsumi0
0
gravatar for Wolfgang Huber
16 days ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

I don't know how to get this to work with GNU binutils. The authoritative source on recommended build configuration is probably https://www.bioconductor.org/checkResults/release/bioc-LATEST/merida1-NodeInfo.html .

On my notebook with MacOS Mojave, R itself and the lypsymphony package build from source with no problems, using Command Line Tools, Xcode, various homebrew packages and the following configure options

export PATH=$PATH:/usr/local/Cellar/texinfo/6.5/bin
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig 
configure \
    --without-internal-tzcode \
    --enable-R-shlib \
    F77=gfortran \
    FC=$F77 \
    CFLAGS='-Wall -mtune=core2 -g' \
    CXXFLAGS='-Wall -mtune=core2 -g -O2' \
    OBJCFLAGS='-Wall -mtune=core2 -g -O2' \
    F77FLAGS='-Wall -g -O2' \
    FCFLAGS=$F77FLAGS
    CC=clang \
    CXX=clang++ \
    OBJC=clang

$ uname -a
Darwin boltzmann.local 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 i386 MacBookPro13,2 Darwin

 

ADD COMMENTlink modified 16 days ago • written 16 days ago by Wolfgang Huber13k

Thank you very much.   I tried the above, but unfortunately, I still have the below error.  I'm quite sure it is the -TP option that's messing things up.   All the best.

 

/usr/local/opt/llvm/bin/clang++ -w -g -O2 -DSYMPHONY_BUILD -TP -o symphony symphony-main.o -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -Wl,-bind_at_load  -L/usr/local/opt/openssl/lib -L/usr/local/opt/libxml2/lib -L/usr/local/opt/libxslt/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/v8@3.15/lib -L/usr/local/opt/llvm/lib -L/usr/local/opt/zlib/lib -L/usr/local/opt/sqlite/lib -L/usr/local/opt/qt/lib ./.libs/libSym.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/Cgl/src/.libs/libCgl.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/Clp/src/OsiClp/.libs/libOsiClp.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/Clp/src/.libs/libClpSolver.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/Clp/src/.libs/libClp.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/Osi/src/Osi/.libs/libOsi.a /Users/tohsumi/Desktop/lpsymphony-master/src/SYMPHONY/CoinUtils/src/.libs/libCoinUtils.a
ld: unknown option: -T
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [symphony] Error 1

 

 

 

ADD REPLYlink written 10 days ago by tohsumi0
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