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'

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

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")

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'