[R-SIG-Mac] 64 bit R tcltk library problem: Symbol not found: _Tk_Init
Steven McKinney
smckinney at bccrc.ca
Thu Nov 6 21:46:30 CET 2008
> 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/tcltk.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/tcltk.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/downloaded_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/tcltk.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.dylib -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/downloaded_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
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