[Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
Michael Felt
aixtools at gmail.com
Wed Jan 6 08:25:09 CET 2016
On 05-Jan-16 08:15, Michael Felt wrote:
> On 04-Jan-16 15:52, Simon Urbanek wrote:
>> No, no duplicate warnings.
I am still getting many duplicate warnings, but am getting farther than
before: such as:
======= 64-bit ending ======== - what is internal error 5 in R_compress3
============
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG
-I/usr/local/include -g -c MASS.c -o MASS.o
xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG
-I/usr/local/include -g -c lqs.c -o lqs.o
xlc_r -qarch=pwr5 -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc
-L/home/cran/64/R/lib -L/opt/lib -liconv -o MASS.so MASS.o lqs.o -lm
-L/home/cran/64/R/lib -lR
ld: 0711-224 WARNING: Duplicate symbol: p_xargc
ld: 0711-224 WARNING: Duplicate symbol: p_xargv
ld: 0711-224 WARNING: Duplicate symbol: p_xrcfg
ld: 0711-224 WARNING: Duplicate symbol: p_xrc
ld: 0711-224 WARNING: Duplicate symbol: end
ld: 0711-224 WARNING: Duplicate symbol: .log
ld: 0711-224 WARNING: Duplicate symbol: log
ld: 0711-224 WARNING: Duplicate symbol: .sqrt
ld: 0711-224 WARNING: Duplicate symbol: sqrt
ld: 0711-224 WARNING: Duplicate symbol: guesses
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-224 WARNING: Duplicate symbol: .isnan
ld: 0711-224 WARNING: Duplicate symbol: isnan
ld: 0711-224 WARNING: Duplicate symbol: .pow
ld: 0711-224 WARNING: Duplicate symbol: pow
ld: 0711-224 WARNING: Duplicate symbol: .exp
ld: 0711-224 WARNING: Duplicate symbol: exp
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
Target "all" is up to date.
installing to /home/cran/64/R/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii,
compress, :
internal error 5 in R_compress3
ERROR: lazydata failed for package 'MASS'
* removing '/home/cran/64/R/library/MASS'
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
cran at x068:[/home/cran/64/R]
========== 32-bit ending -- never ran "out of stack space" - like this -
when using gcc/gfortran, but maybe it is just different ========
xlc_r -qarch=pwr5 -I/home/cran/32/R/include -DNDEBUG
-I../Include -I../../SuiteSparse_config -I/usr/local/include -g
-I../Include -DDINT -c amd_global.c -o amd_i_global.o
xlc_r -qarch=pwr5 -I/home/cran/32/R/include -DNDEBUG
-I../Include -I../../SuiteSparse_config -I/usr/local/include -g
-I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o
amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o
amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o
amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o
amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o
amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o
Target "lib" is up to date.
xlc_r -qarch=pwr5 -I/home/cran/32/R/include -DNDEBUG -DNTIMER
-I/usr/local/include -g -c SuiteSparse_config.c -o
SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
Target "library" is up to date.
xlc_r -qarch=pwr5 -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc
-L/home/cran/32/R/lib -L/opt/lib -liconv -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
abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a
-L/home/cran/32/R/lib -lRlapack -liconv -lxlf90
-L/opt/IBM/xlmass/8.1.2/lib/aix61 -L/opt/IBM/xlf/15.1.2/lib -lxlopt
-lxlipa -lxlf -lxlomp_ser -lpthreads -lm -lm -L/home/cran/32/R/lib -lR
ld: 0711-224 WARNING: Duplicate symbol: p_xargc
ld: 0711-224 WARNING: Duplicate symbol: p_xargv
ld: 0711-224 WARNING: Duplicate symbol: p_xrcfg
ld: 0711-224 WARNING: Duplicate symbol: p_xrc
ld: 0711-224 WARNING: Duplicate symbol: end
ld: 0711-224 WARNING: Duplicate symbol: .bcopy
ld: 0711-224 WARNING: Duplicate symbol: bcopy
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-224 WARNING: Duplicate symbol: .sqrt
ld: 0711-224 WARNING: Duplicate symbol: sqrt
ld: 0711-224 WARNING: Duplicate symbol: guesses
ld: 0711-224 WARNING: Duplicate symbol: .ceil
ld: 0711-224 WARNING: Duplicate symbol: ceil
ld: 0711-224 WARNING: Duplicate symbol: .nearest
ld: 0711-224 WARNING: Duplicate symbol: .nearbyint
ld: 0711-224 WARNING: Duplicate symbol: .trunc
ld: 0711-224 WARNING: Duplicate symbol: .floor
ld: 0711-224 WARNING: Duplicate symbol: .fetestexcept
ld: 0711-224 WARNING: Duplicate symbol: fetestexcept
ld: 0711-224 WARNING: Duplicate symbol: .feraiseexcept
ld: 0711-224 WARNING: Duplicate symbol: .feclearexcept
ld: 0711-224 WARNING: Duplicate symbol: feclearexcept
ld: 0711-224 WARNING: Duplicate symbol: .isnan
ld: 0711-224 WARNING: Duplicate symbol: isnan
ld: 0711-224 WARNING: Duplicate symbol: .strcpy
ld: 0711-224 WARNING: Duplicate symbol: strcpy
ld: 0711-224 WARNING: Duplicate symbol: .log
ld: 0711-224 WARNING: Duplicate symbol: log
ld: 0711-224 WARNING: Duplicate symbol: .dgemm
ld: 0711-224 WARNING: Duplicate symbol: dgemm
ld: 0711-224 WARNING: Duplicate symbol: .exp
ld: 0711-224 WARNING: Duplicate symbol: exp
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
Target "all" is up to date.
installing to /home/cran/32/R/library/Matrix/libs
** R
Warning: unable to re-encode 'Summary.R' line 183
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'image' from package 'graphics' in
package 'Matrix'
Creating a generic function for 'solve' from package 'base' in package
'Matrix'
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in
package 'Matrix'
Creating a generic function for 'determinant' from package 'base' in
package 'Matrix'
Creating a generic function for 'update' from package 'stats' in package
'Matrix'
Creating a generic function for 'as.vector' from package 'base' in
package 'Matrix'
Creating a generic function for 't' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package
'Matrix'
Creating a generic function for 'as.matrix' from package 'base' in
package 'Matrix'
Creating a generic function for 'as.array' from package 'base' in
package 'Matrix'
Creating a generic function for 'head' from package 'utils' in package
'Matrix'
Creating a generic function for 'tail' from package 'utils' in package
'Matrix'
Creating a generic function for 'drop' from package 'base' in package
'Matrix'
Creating a generic function for 'mean' from package 'base' in package
'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in
package 'Matrix'
Creating a generic function for 'isSymmetric' from package 'base' in
package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package
'Matrix'
Creating a generic function for 'chol' from package 'base' in package
'Matrix'
Creating a generic function for 'norm' from package 'base' in package
'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package
'Matrix'
Creating a generic function for 'all.equal' from package 'base' in
package 'Matrix'
Creating a generic function for 'diff' from package 'base' in package
'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"
Creating a generic function for 'colSums' from package 'base' in package
'Matrix'
Creating a generic function for 'colMeans' from package 'base' in
package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package
'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in
package '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 generic function for 'zapsmall' from package 'base' in
package 'Matrix'
Creating a generic function for 'qr' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package
'Matrix'
Creating a generic function for 'crossprod' from package 'base' in
package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in
package 'Matrix'
Creating a generic function for 'print' from package 'base' in package
'Matrix'
Creating a generic function for 'summary' from package 'base' in package
'Matrix'
Creating a generic function for 'which' from package 'base' in package
'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 '"graph","Matrix"': 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 generic function for 'format' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.R' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in
package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in
package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in
package 'Matrix'
** help
*** installing help indices
** building package indices
Loading required package: Matrix
Error: C stack usage 1221002169 is too close to the limit
*** caught segfault ***
address c4866d8c, cause 'memory not mapped'
Traceback:
1: structure(list(message = as.character(message), call = call),
class = class)
2: simpleError(msg, call)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch))) call <- sys.call(-4L) dcall <-
deparse(call)[1L] prefix <- paste("Error in", dcall, ": ")
LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg,
"\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
type = "w") if (is.na(w)) w <- 14L + nchar(dcall,
type = "b") + nchar(sm[1L], type = "b") if (w >
LONG) prefix <- paste0(prefix, "\n ") } else prefix
<- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) { cat(msg,
file = stderr()) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))})
6: try(.install_package_indices(".", instdir))
7: do_install_source(pkg_name, instdir, pkg, desc)
8: do_install(pkg)
9: tools:::.install_packages()
aborting ...
/home/cran/32/R/bin/INSTALL[34]: 14942332 Segmentation fault(coredump)
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
cran at x068:[/home/cran/32/R]
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