[R-SIG-Mac] 64 bit R tcltk library problem: Symbol not found: _Tk_Init

Loren Engrav engrav at u.washington.edu
Fri Nov 7 21:16:39 CET 2008


In December 2007 I put 64bit on a PPC (And in fact you helped me)

Anyway I encountered the same error
And can't remember the exact fix
And am now on Intel 64bit Leopard

But I vaguely remember a path problem

It you follow the path
/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so
does the file tcltk.so exist at that location?

If so if in terminal you cd to /usr/local/bin
Does R -> /Library/Frameworks/R.framework/Resources/R exist at that
location?

And if in terminal you echo $PATH
Does /usr/local/bin show up?

I remember having to be sure usr/local/bin had the right stuff and that
everything knew where everything else was located



> From: Steven McKinney <smckinney at bccrc.ca>
> Date: Thu, 6 Nov 2008 12:46:30 -0800
> To: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
> Subject: [R-SIG-Mac] 64 bit R tcltk library problem: Symbol not found:
> _Tk_Init
> 
> 
> 
>> From the thread
>> "Re: [R-SIG-Mac] 64-bit build of R crashes while idle"
>> Nonetheless any feedback on 64-bit R.app is highly appreciated since
>> not many users appear to use it. Clearly, the more feedback we get the
>> better we can make it.
> 
> I really appreciate all the effort Simon Urbanek and others have
> put into moving along the development and deployment of
> 64 bit R for Mac OS X.
> 
> I installed 64 bit R from  http://r.research.att.com/
> using the command line approach:
>   Leopard builds can be installed as follows - paste in Terminal (for R
> 2.8.x):
>   curl -s http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz |
> sudo tar fvxz - -C /
> 
> I then installed R.app from R-GUI-5256-2.8-leopard-Deployment64.dmg
> and installed a number of bioconductor libraries from source.
> I advanced farther in getting 64-bit R and libraries up and
> running than at any previous attempt, and thought I finally had
> functional 64 bit R available on my Mac.
> 
> But I keep hitting a tcltk problem that I can't seem to solve.
> Whenever I'm trying to install a package that requires tcltk
> the installation fails with this message:
> 
> Loading required package: tcltk
> Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so':
>   
> dlopen(/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tclt
> k.so, 10): Symbol not found: _Tk_Init
>   Referenced from:
> /Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so
>   Expected in: dynamic lookup
> 
> Error : .onLoad failed in 'loadNamespace' for 'tcltk'
> Error: package 'tcltk' could not be loaded
> Execution halted
> 
> Any ideas on how to solve this one?  Any clues as to whether
> I have set something up incorrectly?
> 
> (64 bit R on Leopard appears tantalizingly close!)
> 
> 
> Details:
> I also installed 
> GTK+ 2.10.11 run-time gtk2-runtime.dmg
> Graphviz 2.12 graphviz-2.12.dmg
> gcc 4.2 
> Dapple:gcc-4.2-5564 stevenmckinney$ gcc-4.2 --version
> powerpc-apple-darwin8-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5564)
> 
> gfortran 4.2 gfortran-4.2.3.dmg
> 
> 
> (also RSwitch RSwitch-1.1.dmg though probably not relevant here,
> but I've tried to ensure that all of the myriad development tools
> are installed as per instructions across the various R CRAN and
> r.research.att.com webpages.)
> 
> Initially I installed several Bioconductor packages,
> using biocLite() e.g.
> biocLite("beadarray", type = "source")
> 
> that all went well, with packages compiling with arch ppc64
> etc. (R.app package installer also appears to be working
> beautifully for installing packages from Bioconductor (source).)
> 
> Then a package needing tcltk capabilities tried loading the
> tcltk library, and problems were revealed.  I have tried to ensure
> that I have all tools related to tcltk installed but as yet to
> no avail.
> 
> Here is the issue I keep hitting:
> 
>> install.packages("tcltk2", type = "source")
> trying URL 'http://cran.stat.sfu.ca/src/contrib/tcltk2_1.0-7.tar.gz'
> Content type 'application/x-gzip' length 2083269 bytes (2.0 Mb)
> opened URL
> ==================================================
> downloaded 2.0 Mb
> 
> * Installing *source* package 'tcltk2' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: tcltk
> Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so':
>   
> dlopen(/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tclt
> k.so, 10): Symbol not found: _Tk_Init
>   Referenced from:
> /Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so
>   Expected in: dynamic lookup
> 
> Error : .onLoad failed in 'loadNamespace' for 'tcltk'
> Error: package 'tcltk' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'tcltk2'
> ** Removing '/Library/Frameworks/R.framework/Resources/library/tcltk2'
> 
> The downloaded packages are in
> /private/var/folders/4q/4qrd+OVfHLOrqZ6iI1mrA++++TI/-Tmp-/RtmpYZf9v0/downloade
> d_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("tcltk2", type = "source") :
>   installation of package 'tcltk2' had non-zero exit status
>> sessionInfo()
> R version 2.8.0 Patched (2008-11-05 r46843)
> powerpc-apple-darwin9.5.0
> 
> locale:
> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_2.8.0
>> 
> 
> 
> 
> Here's another example from an attempt to install package 'affy'
> using R.app R Package Installer from Bioconductor (sources):
> 
> * Installing *source* package 'widgetTools' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: tcltk
> Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so':
>   
> dlopen(/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tclt
> k.so, 10): Symbol not found: _Tk_Init
>   Referenced from:
> /Library/Frameworks/R.framework/Resources/library/tcltk/libs/ppc64/tcltk.so
>   Expected in: dynamic lookup
> 
> Error : .onLoad failed in 'loadNamespace' for 'tcltk'
> Error: package 'tcltk' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'widgetTools'
> ** Removing '/Library/Frameworks/R.framework/Resources/library/widgetTools'
> 
> 
> 
> 
> 
> 
> Installing packages that don't require tcltk seems to be working
> very well.  I include a chunk of output should it be useful
> in diagnosing issues:
> 
>> install.packages("Matrix", type = "source")
> trying URL 'http://cran.stat.sfu.ca/src/contrib/Matrix_0.999375-16.tar.gz'
> Content type 'application/x-gzip' length 1943837 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
> 
> * Installing *source* package 'Matrix' ...
> ** libs
> ** arch - ppc64
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c CHMfactor.c -o CHMfactor.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c Csparse.c -o Csparse.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c TMatrix_as.c -o TMatrix_as.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c Tsparse.c -o Tsparse.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c Mutils.c -o Mutils.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c chm_common.c -o chm_common.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c cs.c -o cs.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c cs_utils.c -o cs_utils.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dense.c -o dense.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dgCMatrix.c -o dgCMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dgTMatrix.c -o dgTMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dgeMatrix.c -o dgeMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dpoMatrix.c -o dpoMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dppMatrix.c -o dppMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dsCMatrix.c -o dsCMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dsyMatrix.c -o dsyMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dspMatrix.c -o dspMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dtCMatrix.c -o dtCMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dtTMatrix.c -o dtTMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dtrMatrix.c -o dtrMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c dtpMatrix.c -o dtpMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c factorizations.c -o factorizations.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c ldense.c -o ldense.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c lgCMatrix.c -o lgCMatrix.o
> gcc-4.2 -arch ppc64 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I./UFconfig
> -I/usr/local/include    -fPIC  -g -O2 -c sparseQR.c -o sparseQR.o
> ( cd Lib ; make clean )
> ( cd Lib ; make clean )
> ( cd Source ; make clean )
> ( cd Source ; make clean )
> ( cd Lib ; make lib )
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_rmap.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/SuiteSparseQR_C.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/SuiteSparseQR_expert.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_parallel.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_kernel.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_analyze.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_assemble.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_cpack.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_csize.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_fcsize.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_debug.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_front.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_factorize.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_freenum.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_freesym.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_freefac.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_fsize.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_maxcolnorm.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_rconvert.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_rcount.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_rhpack.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_rsolve.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_stranspose1.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_stranspose2.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_hpinv.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_1fixed.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_1colamd.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/SuiteSparseQR.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_1factor.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_cumsum.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_shift.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_happly.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_panel.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_happly_work.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/SuiteSparseQR_qmult.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_trapezoidal.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_larftb.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_append.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_type.cpp
> g++-4.2 -arch ppc64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64 -I../../UFconfig
> -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
> -fPIC  -g -O2  -c ../Source/spqr_tol.cpp
> ar -rucs ../../SPQR.a spqr_rmap.o SuiteSparseQR_C.o SuiteSparseQR_expert.o
> spqr_parallel.o spqr_kernel.o spqr_analyze.o spqr_assemble.o spqr_cpack.o
> spqr_csize.o spqr_fcsize.o spqr_debug.o spqr_front.o spqr_factorize.o
> spqr_freenum.o spqr_freesym.o spqr_freefac.o spqr_fsize.o spqr_maxcolnorm.o
> spqr_rconvert.o spqr_rcount.o spqr_rhpack.o spqr_rsolve.o spqr_stranspose1.o
> spqr_stranspose2.o spqr_hpinv.o spqr_1fixed.o spqr_1colamd.o SuiteSparseQR.o
> spqr_1factor.o spqr_cumsum.o spqr_shift.o spqr_happly.o spqr_panel.o
> spqr_happly_work.o SuiteSparseQR_qmult.o spqr_trapezoidal.o spqr_larftb.o
> spqr_append.o spqr_type.o spqr_tol.o
> ranlib: file: ../../SPQR.a(spqr_parallel.o) has no symbols
> ranlib: file: ../../SPQR.a(spqr_debug.o) has no symbols
> ( cd Lib ; make )
> .
> .
> .
> g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names  -undefined
> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o
> Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o
> chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o
> dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o
> dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o
> sparseQR.o SPQR.a CHOLMOD.a COLAMD.a AMD.a
> -L/Library/Frameworks/R.framework/Resources/lib/ppc64 -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib/ppc64 -lRblas -lgfortran
> -lSystemStubs  -L/Library/Frameworks/R.framework/Resources/lib/ppc64 -lR
> -dylib_file 
> libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc64/libRblas.dy
> lib -Wl,-framework -Wl,CoreFoundation
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Loading required package: lattice
> Creating a generic for "rcond" in package  "Matrix"
>     (the supplied definition differs from and overrides the implicit generic
> in package "base": Formal arguments differ: (x, norm, ...), (x, norm,
> triangular, ...))
> Creating a generic for "colSums" in package  "Matrix"
>     (the supplied definition differs from and overrides the implicit generic
> in package "base": Formal arguments differ: (x, na.rm, dims, ...), (x, na.rm,
> dims))
> Creating a generic for "colMeans" in package  "Matrix"
>     (the supplied definition differs from and overrides the implicit generic
> in package "base": Formal arguments differ: (x, na.rm, dims, ...), (x, na.rm,
> dims))
> Creating a generic for "rowSums" in package  "Matrix"
>     (the supplied definition differs from and overrides the implicit generic
> in package "base": Formal arguments differ: (x, na.rm, dims, ...), (x, na.rm,
> dims))
> Creating a generic for "rowMeans" in package  "Matrix"
>     (the supplied definition differs from and overrides the implicit generic
> in package "base": Formal arguments differ: (x, na.rm, dims, ...), (x, na.rm,
> dims))
> Creating a new generic function for "image" in "Matrix"
> Creating a new generic function for "solve" in "Matrix"
> Creating a new generic function for "determinant" in "Matrix"
> Creating a new generic function for "update" in "Matrix"
> Creating a new generic function for "crossprod" in "Matrix"
> Creating a new generic function for "tcrossprod" in "Matrix"
> Creating a new generic function for "t" in "Matrix"
> Creating a new generic function for "diag" in "Matrix"
> Creating a new generic function for "as.matrix" in "Matrix"
> Creating a new generic function for "as.array" in "Matrix"
> Creating a new generic function for "head" in "Matrix"
> Creating a new generic function for "tail" in "Matrix"
> Creating a new generic function for "drop" in "Matrix"
> Creating a new generic function for "as.vector" in "Matrix"
> Creating a new generic function for "mean" in "Matrix"
> Creating a new generic function for "cov2cor" in "Matrix"
> Creating a new generic function for "isSymmetric" in "Matrix"
> Creating a new generic function for "unname" in "Matrix"
> Creating a new generic function for "kronecker" in "Matrix"
> Creating a new generic function for "chol" in "Matrix"
> Creating a new generic function for "all.equal" in "Matrix"
> Creating a new generic function for "diff" in "Matrix"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csr"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.coo"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "matrix.csc"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "colSums" no definition for class:
> "igCMatrix"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "rowSums" no definition for class:
> "igCMatrix"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "colMeans" no definition for class:
> "igCMatrix"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "rowMeans" no definition for class:
> "igCMatrix"
> Creating a new generic function for "zapsmall" in "Matrix"
> Creating a new generic function for "qr" in "Matrix"
> Creating a new generic function for "print" in "Matrix"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "graphAM"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "graph"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class:
> "graphNEL"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class: 
> "graphNEL"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class: 
> "graph"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class: 
> "graphNEL"
> Warning in matchSignature(signature, fdef, where) :
>   in the method signature for function "coerce" no definition for class: 
> "graphNEL"
> Creating a new generic function for "summary" in "Matrix"
> Creating a new generic function for "qr.R" in "Matrix"
> Creating a new generic function for "qr.qy" in "Matrix"
> Creating a new generic function for "qr.qty" in "Matrix"
> Creating a new generic function for "qr.coef" in "Matrix"
> Creating a new generic function for "qr.resid" in "Matrix"
> Creating a new generic function for "qr.fitted" in "Matrix"
> ** help
>>>> Building/Updating help pages for package 'Matrix'
>      Formats: text html latex example 
>   BunchKaufman-methods              text    html    latex   example
>   CAex                              text    html    latex   example
>   CHMfactor-class                   text    html    latex   example
>   Cholesky-class                    text    html    latex   example
>   Cholesky                          text    html    latex   example
>   CsparseMatrix-class               text    html    latex   example
>   Diagonal                          text    html    latex   example
>   Hilbert                           text    html    latex   example
>   KNex                              text    html    latex   example
>   LU-class                          text    html    latex   example
>   Matrix-class                      text    html    latex   example
>   Matrix                            text    html    latex   example
>   MatrixFactorization-class         text    html    latex   example
>   RsparseMatrix-class               text    html    latex   example
>   Schur-class                       text    html    latex   example
>   Schur                             text    html    latex   example
>   SparseM-conv                      text    html    latex
>   Subassign-methods                 text    html    latex   example
>   TsparseMatrix-class               text    html    latex   example
>   USCounties                        text    html    latex   example
>   Xtrct-methods                     text    html    latex   example
>   all-methods                       text    html    latex   example
>   all.equal-methods                 text    html    latex   example
>   atomicVector-class                text    html    latex   example
>   band                              text    html    latex   example
>   bdiag                             text    html    latex   example
>   cBind                             text    html    latex   example
>   chol                              text    html    latex   example
>   colSums                           text    html    latex   example
>   compMatrix-class                  text    html    latex
>   dMatrix-class                     text    html    latex   example
>   ddenseMatrix-class                text    html    latex   example
>   ddiMatrix-class                   text    html    latex   example
>   denseMatrix-class                 text    html    latex   example
>   dgCMatrix-class                   text    html    latex   example
>   dgRMatrix-class                   text    html    latex
>   dgTMatrix-class                   text    html    latex   example
>   dgeMatrix-class                   text    html    latex
>   diagonalMatrix-class              text    html    latex   example
>   dpoMatrix-class                   text    html    latex   example
>   drop0                             text    html    latex   example
>   dsCMatrix-class                   text    html    latex   example
>   dsRMatrix-class                   text    html    latex   example
>   dsparseMatrix-class               text    html    latex   example
>   dsyMatrix-class                   text    html    latex   example
>   dtCMatrix-class                   text    html    latex   example
>   dtRMatrix-class-def               text    html    latex   example
>   dtpMatrix-class                   text    html    latex   example
>   dtrMatrix-class                   text    html    latex   example
>   expand                            text    html    latex   example
>   expm                              text    html    latex   example
>   externalFormats                   text    html    latex   example
>   facmul                            text    html    latex   example
>   forceSymmetric                    text    html    latex   example
>   generalMatrix-class               text    html    latex
>   image-methods                     text    html    latex   example
>   index-class                       text    html    latex   example
>   is.na-methods                     text    html    latex   example
>   isSymmetric-methods               text    html    latex
>   kronecker-methods                 text    html    latex   example
>   ldenseMatrix-class                text    html    latex   example
>   ldiMatrix-class                   text    html    latex   example
>   lgeMatrix-class                   text    html    latex   example
>   lsparseMatrix-classes             text    html    latex   example
>   lsyMatrix-class                   text    html    latex   example
>   ltrMatrix-class                   text    html    latex   example
>   lu                                text    html    latex   example
>   nMatrix-class                     text    html    latex   example
>   ndenseMatrix-class                text    html    latex   example
>   nearPD                            text    html    latex   example
>   ngeMatrix-class                   text    html    latex   example
>   nnzero                            text    html    latex   example
>   norm                              text    html    latex   example
>   nsparseMatrix-classes             text    html    latex   example
>   nsyMatrix-class                   text    html    latex   example
>   ntrMatrix-class                   text    html    latex   example
>   number-class                      text    html    latex   example
>   pMatrix-class                     text    html    latex   example
>   printSpMatrix                     text    html    latex   example
>   qr-methods                        text    html    latex
>   rcond                             text    html    latex   example
>   replValue-class                   text    html    latex   example
>   spMatrix                          text    html    latex   example
>   sparseLU-class                    text    html    latex   example
>   sparseMatrix-class                text    html    latex   example
>   sparseQR-class                    text    html    latex   example
>   sparseVector-class                text    html    latex   example
>   symmetricMatrix-class             text    html    latex   example
>   symmpart                          text    html    latex   example
>   tcrossprod                        text    html    latex   example
>   triangularMatrix-class            text    html    latex   example
>   unpack                            text    html    latex   example
>   unused-classes                    text    html    latex   example
>   xtabs                             text    html    latex   example
> ** building package indices ...
> Loading required package: Matrix
> Loading required package: stats
> Loading required package: methods
> Loading required package: lattice
> 
> Attaching package: 'Matrix'
> 
> 
> The following object(s) are masked from package:stats :
> 
> xtabs 
> 
> 
> The following object(s) are masked from package:base :
> 
> colMeans,
> colSums,
> rcond,
> rowMeans,
> rowSums 
> 
> * DONE (Matrix)
> 
> The downloaded packages are in
> /private/var/folders/4q/4qrd+OVfHLOrqZ6iI1mrA++++TI/-Tmp-/RtmpYZf9v0/downloade
> d_packages
> Updating HTML index of packages in '.Library'
>> 
> 
> 
> Steven McKinney
> 
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
> 
> email: smckinney +at+ bccrc +dot+ ca
> 
> tel: 604-675-8000 x7561
> 
> BCCRC
> Molecular Oncology
> 675 West 10th Ave, Floor 4
> Vancouver B.C. 
> V5Z 1L3
> Canada
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac



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