Question: [XPS]Installation of xps package in macOS Sierra
0
gravatar for snj
2.7 years ago by
snj0
snj0 wrote:

Hi all,

 

I have been trying to install xps package in my PC (macOS Sierra 10.12.3).

I have tried many ways in references to the posts in this support and the web sites.

But, I can not install xps successfully.

1. System Integrity Protection was disabled.

2. ROOT (v5.34.36_2) was installed using Homebrew. (I could not make root5 from source.)

 I moved the ROOT folder in home folder and .bashrc was set.  ROOT seems to work well.

3. R (v3.3.2) was started in Terminal and I tried to install xps (v1.34.0) both from biocLite and a downloaded source.

I aslo tried to install from a downloaded source from Terminal by "R CMD INSTALL xps_1.34.0.tar.gz".

 

Error message is below. Please tell me the way to install xps.

 

27 warnings generated.

clang++ -dynamiclib -single_module -undefined dynamic_lookup -install_name /private/var/folders/dz/165_0y8x4q9d9f6gv3nkjblw0000gq/T/RtmpvolO4o/R.INSTALL5196737075cf/xps/src/xps.dylib -O2 -m64 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/usr/local/Cellar/root/5.34.36_2/lib/root -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -stdlib=libc++ -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.dylib

clang++ -bundle -undefined dynamic_lookup -O2 -m64 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o \

           -o  xps.so

installing to /usr/local/lib/R/3.3/site-library/xps/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/usr/local/lib/R/3.3/site-library/xps/libs/xps.so':

  dlopen(/usr/local/lib/R/3.3/site-library/xps/libs/xps.so, 6): Symbol not found: __ZN4ROOT17TGenericClassInfoD1Ev

  Referenced from: /usr/local/lib/R/3.3/site-library/xps/libs/xps.so

  Expected in: flat namespace

 in /usr/local/lib/R/3.3/site-library/xps/libs/xps.so

Error: loading failed

Execution halted

ERROR: loading failed

* removing '/usr/local/lib/R/3.3/site-library/xps'

xps package installation • 812 views
ADD COMMENTlink modified 2.7 years ago by Martin Morgan ♦♦ 23k • written 2.7 years ago by snj0
Answer: [XPS]Installation of ups package in macOS Sierra
2
gravatar for cstrato
2.7 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:

Hi,

Since you are using Mac OS Sierra, things are more complicated since:
1, the 'xps' binary which you can download from BioC was created for Mavericks and may not work on Sierra
2, There does not exist a binary of ROOT for Sierra, so you need to compile ROOT yourself.

You can (and should) use the latest version of R, i.e. R-3.3.2

However, you need to download the source code of 'xps' from BioC development, 
since only this version will work with Sierra, i.e.:
bioconductor.org/packages/3.5/bioc/src/contrib/xps_1.35.2.tar.gz

You need to download the source code of the following ROOT version, i.e.:
https://root.cern.ch/download/root_v5.34.36.source.tar.gz

Note: Do NOT use any ROOT version using Homebrew!!!

Please read the README file of the development version of xps how to install ROOT on Sierra, i.e.:
http://bioconductor.org/packages/3.5/bioc/readmes/xps/README

The relevant chapters of README are Ie and then Id.

Note:
There may be an additional possibility, with which another user of xps did succeed,
however I did not test it.
- install on Sierra Xcode 7.3.1 instead of Xcode 8.1
- disable SIP using 'csrutil disable'
- then you can download the root version compiled with Xcode 7 from:
 https://root.cern.ch/download/root_v5.34.36.macosx64-10.11-clang70.tar.gz
 (alternatively you need to compile root from source)
- then you should be able to R CMD INSTALL xps_1.34.0.tgz

Regards,
Christian

 

ADD COMMENTlink written 2.7 years ago by cstrato3.9k

Thank you very much, Christian!

I have successfully installed ROOT and xps on my Sierra machine.

 

ADD REPLYlink written 2.7 years ago by snj0
Answer: [XPS]Installation of ups package in macOS Sierra
0
gravatar for zqzneptune
2.7 years ago by
zqzneptune0
zqzneptune0 wrote:

Hi,

I'm also using macOS Sierra. You don't necessarily have to install from source, just use Bioconductor biocLite to install would be fine since there is binary version available.

source("http://bioconductor.org/biocLite.R")

biocLite("xps")

 

 

ADD COMMENTlink written 2.7 years ago by zqzneptune0
Answer: [XPS]Installation of ups package in macOS Sierra
0
gravatar for snj
2.7 years ago by
snj0
snj0 wrote:

Thank you, zqzneptune.

I have already tried to install biocLite binary version.

I tried the procedure again, but could not install it with the same error massages.

 

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/usr/local/lib/R/3.3/site-library/xps/libs/xps.so':

  dlopen(/usr/local/lib/R/3.3/site-library/xps/libs/xps.so, 6): Symbol not found: __ZN4ROOT17TGenericClassInfoD1Ev

  Referenced from: /usr/local/lib/R/3.3/site-library/xps/libs/xps.so

  Expected in: flat namespace

 in /usr/local/lib/R/3.3/site-library/xps/libs/xps.so

Error: loading failed

Execution halted

ERROR: loading failed

* removing '/usr/local/lib/R/3.3/site-library/xps'

 

ADD COMMENTlink written 2.7 years ago by snj0

I have done clean install of macOS and updated to macOS Sierra.

I have installed Xcode (command line), xquartz, then homebrewed root (v5) and r (v3.3.2).

I tried again to install xps (biocLite("xps")), but the same error messages came...

ADD REPLYlink written 2.7 years ago by snj0
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