> 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 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
