[R-SIG-Mac] problems compiling R 2.11.1 on OSX 10.5.8
Michael Lachmann
lachmann at eva.mpg.de
Mon Aug 2 20:32:45 CEST 2010
I tried installing 2.11.1 from the sources, and encountered a problem
with package Matrix. I simply used
./configure
make
And my system has fink installed.
Below are the errors I encountered:
---
[...up to here all was ok...]
* DONE (lattice)
begin installing recommended package Matrix
* installing *source* package ‘Matrix’ ...
** libs
gcc -std=gnu99 -I[DIR]/R-2.11.1/include -I./UFconfig -I/sw/include
-I/usr/local/include -fPIC -g -O2 -c CHMfactor.c -o CHMfactor.o
[... some more successful compiles...]
ar -rucs ../../AMD.a amd_global.o amd_l_1.o amd_l_2.o amd_l_aat.o
amd_l_control.o amd_l_defaults.o amd_l_dump.o amd_l_info.o
amd_l_order.o amd_l_post_tree.o amd_l_postorder.o amd_l_preprocess.o
amd_l_valid.o # amd_i_1.o amd_i_2.o amd_i_aat.o amd_i_control.o
amd_i_defaults.o amd_i_dump.o amd_i_info.o amd_i_order.o
amd_i_post_tree.o amd_i_postorder.o amd_i_preprocess.o amd_i_valid.o
ranlib: file: ../../AMD.a(amd_l_dump.o) has no symbols
[...some more things that look ok...]
installing to [DIR]/R-2.11.1/library/Matrix/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "image" in "Matrix"
Creating a new generic function for "solve" in "Matrix"
Restoring the implicit generic function for ‘chol2inv’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, size, LINPACK), (x, ...))
Creating a new generic function for "chol2inv" 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 "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"
Restoring the implicit generic function for ‘norm’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, type), (x, type, ...))
Creating a new generic function for "norm" in "Matrix"
Restoring the implicit generic function for ‘rcond’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, norm, triangular, ...), (x,
norm, ...))
Creating a new generic function for "rcond" in "Matrix"
Creating a new generic function for "all.equal" in "Matrix"
Creating a new generic function for "diff" in "Matrix"
in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no
definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no
definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no
definition for class "matrix.csc"
in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no
definition for class "matrix.csc"
in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no
definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no
definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"dsparseMatrix","matrix.csr"’:
no definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.csr","dgCMatrix"’: no
definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.coo","dgCMatrix"’: no
definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"matrix.csr","RsparseMatrix"’:
no definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’:
no definition for class "matrix.csc"
in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’:
no definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’:
no definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.coo","CsparseMatrix"’:
no definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"matrix.csc","TsparseMatrix"’:
no definition for class "matrix.csc"
in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’:
no definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csr"’:
no definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.coo"’:
no definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csc"’:
no definition for class "matrix.csc"
in method for ‘coerce’ with signature ‘"matrix.csr","Matrix"’: no
definition for class "matrix.csr"
in method for ‘coerce’ with signature ‘"matrix.coo","Matrix"’: no
definition for class "matrix.coo"
in method for ‘coerce’ with signature ‘"matrix.csc","Matrix"’: no
definition for class "matrix.csc"
Restoring the implicit generic function for ‘colSums’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, na.rm, dims), (x, na.rm,
dims, ...))
Creating a new generic function for "colSums" in "Matrix"
Restoring the implicit generic function for ‘colMeans’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, na.rm, dims), (x, na.rm,
dims, ...))
Creating a new generic function for "colMeans" in "Matrix"
Restoring the implicit generic function for ‘rowSums’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, na.rm, dims), (x, na.rm,
dims, ...))
Creating a new generic function for "rowSums" in "Matrix"
Restoring the implicit generic function for ‘rowMeans’ from package ‘base’
into package ‘Matrix’; the generic differs from the default
conversion (Formal arguments differ: (x, na.rm, dims), (x, na.rm,
dims, ...))
Creating a new generic function for "rowMeans" in "Matrix"
in method for ‘colSums’ with signature ‘x="igCMatrix"’: no definition
for class "igCMatrix"
in method for ‘rowSums’ with signature ‘x="igCMatrix"’: no definition
for class "igCMatrix"
in method for ‘colMeans’ with signature ‘x="igCMatrix"’: no definition
for class "igCMatrix"
in method for ‘rowMeans’ with signature ‘x="igCMatrix"’: 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 "crossprod" in "Matrix"
Creating a new generic function for "tcrossprod" in "Matrix"
Creating a new generic function for "print" in "Matrix"
Creating a new generic function for "which" in "Matrix"
in method for ‘coerce’ with signature ‘"graphAM","sparseMatrix"’: no
definition for class "graphAM"
in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no
definition for class "graph"
in method for ‘coerce’ with signature ‘"graphNEL","CsparseMatrix"’: no
definition for class "graphNEL"
in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no
definition for class "graphNEL"
in method for ‘coerce’ with signature ‘"sparseMatrix","graph"’: no
definition for class "graph"
in method for ‘coerce’ with signature ‘"sparseMatrix","graphNEL"’: no
definition for class "graphNEL"
in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: 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
*** installing help indices
** building package indices ...
Loading required package: Matrix
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '[DIR]/R-2.11.1/library/Matrix/libs/Matrix.so':
dlopen([DIR]/R-2.11.1/library/Matrix/libs/Matrix.so, 6): Symbol not
found: _cholmod_l_add
Referenced from: [DIR]/R-2.11.1/library/Matrix/libs/Matrix.so
Expected in: dynamic lookup
Error : require(Matrix, save = FALSE) is not TRUE
ERROR: installing package indices failed
* removing ‘[DIR]/R-2.11.1/library/Matrix’
make[2]: *** [Matrix.ts] Error 1
make[1]: *** [recommended-packages] Error 2
thanks,
Michael
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