lgc - Log Gaussian Cox Processes for fish abundance modelling - check results
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lgc

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Version: 1.4
Result: ERROR
Check time: 2018-01-26 15:47
* using log directory ''
* using R Under development (unstable) (2018-01-26 r74168)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'lgc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lgc' version '1.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialized R objects in the sources ... OK
* checking whether package 'lgc' can be installed ... WARNING
Found the following significant warnings:
Warning: in method for 'coerce' with signature '"gridFactor","distFactor"': no definition for classes "gridFactor", "distFactor"
See '00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or later
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
'generateDemoIndex.R'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'DATRAS' 'mapdata' 'maps' 'numDeriv' 'polynom' 'sp'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
boundary:
function(x, ...)
boundary.polygonGrid:
function(x)

c:
function(...)
c.list:
function()

chol:
function(x, ...)
chol.solve:
function(a, b, ...)

plot:
function(x, ...)
plot.fitlgc:
function(fit, which, pattern, cex.axis, ...)

model.matrix:
function(object, ...)
model.matrix.polygons:
function(x, ...)

rstandard:
function(model, ...)
rstandard.fitlgc:
function(model, fixbeta, seed)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
[.distFactor [.gridFactor [.polygonGrid as.data.frame.polygonGrid
as.polygons.polygonGrid as.polygons.polygons boundary.polygonGrid
c.list chol.solve coef.fitlgc cut.polygonGrid fitted.fitlgc
image.polygonGrid image.polygons logLik.fitlgc
model.matrix.polygonGrid model.matrix.polygons plot.fitlgc
plot.polygonGrid plot.polygons print.distFactor print.fitlgc
print.polygons print.triangles rstandard.fitlgc simulate.fitlgc
simulate.fitlgc.old summary.fitlgc summary.polygons vcov.fitlgc
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("CHMfactor_to_sparse", ..., PACKAGE = "Matrix")
.Call("Csparse_submatrix", ..., PACKAGE = "Matrix")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

blockAR1: warning in Reduce(fun, A, init = x0, acc = TRUE): partial
argument match of 'acc' to 'accumulate'
sepGMRFpredict : matvec : rotate: warning in seq.int(length =
length(dim(x))): partial argument match of 'length' to 'length.out'
.lgc_optimize: no visible global function definition for 'grad'
.lgc_optimize: no visible global function definition for 'optim'
GMRFsample: no visible global function definition for 'rnorm'
LRtest: no visible binding for global variable 'logLik'
LRtest: no visible global function definition for 'pchisq'
activateOptMethods : : no visible global function definition for
'cfunction'
blockAR1 : fun: no visible global function definition for 'rnorm'
car2sph: no visible binding for global variable 'y'
car2sph: no visible binding for global variable 'x'
car2sph: no visible binding for global variable 'z'
checkCovStruct: no visible global function definition for 'rnorm'
checkCovStruct: no visible global function definition for 'grad'
coef.fitlgc: no visible global function definition for 'fitted'
colorstrip: no visible global function definition for 'par'
colorstrip: no visible global function definition for 'rect'
covParameter: no visible binding for global variable 'logscale'
covStruct: no visible binding for global variable 'loga'
covStruct: no visible binding for global variable 'logc'
covStruct: no visible global function definition for 'deriv'
covStructFormula : : no visible binding for global variable
'a'
covStructFormula : : no visible binding for global variable
's'
covStructFormula : : no visible binding for global variable
'b'
covStructFormula : : no visible binding for global variable
'I1'
covStructFormula : : no visible binding for global variable
'I2'
covStructFormula : : no visible binding for global variable
'I3'
covStructFormula : : no visible binding for global variable
'I4'
covStructFormula : : no visible global function definition
for 'deriv'
covStructFormula: no visible global function definition for
'model.frame'
covStructFormula: no visible binding for global variable 'na.pass'
covStructFormula: no visible global function definition for
'model.matrix'
covStructFormula: no visible global function definition for 'deriv'
cut.polygonGrid : : no visible global function definition
for 'point.in.polygon'
dist.simple: no visible global function definition for 'dist'
gridLocateBin : recursiveLocate: no visible global function definition
for 'median'
image.polygonGrid: no visible global function definition for
'model.matrix'
image.polygons: no visible global function definition for 'polygon'
plot.fitlgc: no visible global function definition for 'coef'
plot.fitlgc: no visible global function definition for 'vcov'
plot.fitlgc: no visible global function definition for 'axis'
plot.fitlgc: no visible global function definition for 'segments'
plot.fitlgc: no visible global function definition for 'box'
plot.polygonGrid: no visible binding for global variable 'points'
plot.polygons: no visible global function definition for 'polygon'
plot.polygons: no visible global function definition for 'points'
print.polygons: no visible global function definition for 'quantile'
print.triangles: no visible global function definition for 'quantile'
rstandard.fitlgc: no visible global function definition for 'rnorm'
sepGMRFpredict: no visible global function definition for 'rnorm'
simconfint : : no visible global function definition for
'quantile'
simconfint: no visible global function definition for 'vcov'
simconfint: no visible global function definition for 'coef'
simulate.fitlgc: no visible global function definition for 'rnorm'
simulate.fitlgc: no visible global function definition for 'rpois'
simulate.fitlgc.old: no visible global function definition for 'rnorm'
splitMap: no visible binding for global variable 'na.omit'
stat.ARk.prec: no visible global function definition for 'polynomial'
summary.fitlgc: no visible global function definition for 'coef'
summary.fitlgc: no visible global function definition for 'vcov'
summary.fitlgc: no visible global function definition for 'pchisq'
plot,covStruct: no visible global function definition for 'par'
plot,covStruct: no visible binding for global variable 'dist'
plot,covStruct: no visible binding for global variable
'dense.covariance'
simulate,covStruct: no visible binding for global variable 'C'
update,covStruct: no visible binding for global variable 'deriv'
Undefined global functions or variables:
C I1 I2 I3 I4 a axis b box cfunction coef dense.covariance deriv dist
fitted grad logLik loga logc logscale median model.frame model.matrix
na.omit na.pass optim par pchisq point.in.polygon points polygon
polynomial quantile rect rnorm rpois s segments vcov x y z
Consider adding
importFrom("graphics", "axis", "box", "par", "points", "polygon",
"rect", "segments")
importFrom("stats", "C", "coef", "deriv", "dist", "fitted", "logLik",
"median", "model.frame", "model.matrix", "na.omit",
"na.pass", "optim", "pchisq", "quantile", "rnorm", "rpois",
"vcov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'Devaluate' 'GMRFdens' 'GMRFextend' 'GMRFmarginal' 'GMRFpredict'
'GMRFreduce' 'GMRFsample' 'GMRFstandard' 'LGMRFpredict' 'ZeroMatrix'
'[.distFactor' '[.gridFactor' '[.polygonGrid' 'addNugget'
'as.data.frame.polygonGrid' 'as.polygons' 'as.polygons.polygonGrid'
'as.polygons.polygons' 'axpyCovStruct' 'axpyCovStruct2'
'bdiagCovStruct' 'block2x2' 'blockAR1' 'blockToList' 'boundary'
'boundary.polygonGrid' 'c.list' 'car2sph' 'carDist' 'checkCovStruct'
'chol.solve' 'circFactor' 'coef.fitlgc' 'colorstrip' 'concTransform'
'connectedComponents' 'cornerMatrix' 'cov2covStruct' 'covDiag'
'covIdent' 'covParameter' 'covStruct' 'covStruct2Cor' 'covStructAR'
'covStructGMRF' 'covStructGeneral' 'covStructNonlin'
'covStructNonlinExtend' 'covStructProj' 'covStructVAR1'
'cut.polygonGrid' 'diagblock2x2' 'dist.all' 'dist.km' 'dist.simple'
'distFactor' 'distkm' 'evaluate' 'extendCovStruct' 'factorToSparse'
'fastPerm' 'fitted.fitlgc' 'fullHessian' 'fullHessian2' 'fullPredict'
'gridLocateBin' 'heatpal' 'image.polygonGrid' 'image.polygons'
'initialHexagon' 'initialSquare' 'levelAttrib' 'levelAttrib<-'
'logLik.fitlgc' 'lyapunov' 'makeMap' 'makeSquares' 'makeTriangles'
'modMat' 'model.matrix.polygonGrid' 'model.matrix.polygons' 'mybdiag'
'na2sparse' 'nearestkm' 'nnb' 'nsidesPolygons' 'obsnum' 'plot.fitlgc'
'plot.polygonGrid' 'plot.polygons' 'polygonGrid' 'print.distFactor'
'print.fitlgc' 'print.polygons' 'print.triangles' 'rectGrid'
'rmLapply' 'scaleCovStruct' 'scatterGrid' 'shave' 'simconfint'
'simulate.fitlgc.old' 'solveSubset' 'sparseSubset' 'sph2car'
'sphDist' 'sphMidpoint' 'sphMoveNorthpole' 'sphRot' 'splitMap'
'splitPolygons' 'splitTriangles' 'squareGrid' 'squareGridSubdiv'
'stat.ARk.prec' 'summary.fitlgc' 'summary.polygons' 'surroundCircle'
'symblock2x2' 'triangularGrid' 'triblock2x2' 'vcov.fitlgc'
'wetEdgeFilter'
Undocumented data sets:
'NorthSeaCod.2009.Q1'
Undocumented S4 classes:
'covStruct' 'lgc_control'
Undocumented S4 methods:
generic '*' and siglist 'dgCMatrix,dgCMatrix'
generic '*' and siglist 'matrix,dgCMatrix'
generic '+' and siglist 'dgCMatrix,matrix'
generic 'cbind2' and siglist 'dgCMatrix,dgeMatrix'
generic 'coerce' and siglist 'dgCMatrix,dsCMatrix'
generic 'coerce' and siglist 'gridFactor,distFactor'
generic 'image' and siglist 'covStruct'
generic 'initialize' and siglist 'covStruct'
generic 'kronecker' and siglist 'covStruct,covStruct'
generic 'kronecker' and siglist 'dgCMatrix,dgCMatrix'
generic 'kronecker' and siglist 'dgCMatrix,dsCMatrix'
generic 'kronecker' and siglist 'sparseMatrix,matrix'
generic 'log' and siglist 'covStruct'
generic 'plot' and siglist 'covStruct'
generic 'show' and siglist 'covStruct'
generic 'simulate' and siglist 'covStruct'
generic 'solveSubset' and siglist 'CHMfactor'
generic 'solveSubset' and siglist 'dgCMatrix'
generic 'solveSubset' and siglist 'dsCMatrix'
generic 'solveSubset' and siglist 'dtCMatrix'
generic 'update' and siglist 'covStruct'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'covStructFormula'
'delta.nonlin' 'scale' 'nonlin' 'parameters' 'denseFixef'
'ignore.proj'

Undocumented arguments in documentation object 'fitlgc'
'denseFixef' 'nonlin' 'parameters' 'ignore.proj' 'optimize' '...'

Undocumented arguments in documentation object 'gridConstruct'
'connected'
Documented arguments not in \usage in documentation object 'gridConstruct':
'center' 'km'

Undocumented arguments in documentation object 'simulate.fitlgc'
'fixbeta'
Documented arguments not in \usage in documentation object 'simulate.fitlgc':
'betafix'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'rstandard.fitlgc':
'rstandard.fitlgc'

S3 methods shown with full name in documentation object 'simulate.fitlgc':
'simulate.fitlgc'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'activateOptMethods':
'on'

Argument items with no description in Rd object 'fitlgc':
'permfun' 'scale'

Argument items with no description in Rd object 'gridConstruct':
'...' 'grid' 'points'

Argument items with no description in Rd object 'simulate.fitlgc':
'...'

* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'lgc/libs/lgc.so':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... ERROR
Running examples in 'lgc-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: covStructFormula
> ### Title: Formula interface to covStructs.
> ### Aliases: covStructFormula
>
> ### ** Examples
>
> ##' === Separable correlation on grid with a nugget effect.
> d <- expand.grid(x=factor(1:7),y=factor(1:8))
> C <- covStructFormula(~AR1(x)*AR1(y)+AR2(y),nugef=~1,fixef=NULL,data=d)
> ##' === Some methods
> C@parameters
transf.AR1(x) transf.AR1(y) corr.AR2(y)1 AR2(y)2 lognugget.
0.54930614 0.54930614 0.03333333 -0.50000000 0.00000000
> simulate(C)
Loading required package: polynom

*** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
1: asMethod(object)
2: as(as(spMatrix(n, n, j = rep(n, n), i = 1:n, x = rep(0, n)), "dgCMatrix"), "dsCMatrix")
3: cov(Q)
4: stat.ARk.prec(phi, n = n)
5: FUN(X[[i]], ...)
6: lapply(X = X, FUN = FUN, ...)
7: sapply(vars, get, envir = e, simplify = FALSE)
8: eval(quote(environment()), sapply(vars, get, envir = e, simplify = FALSE))
9: eval(expr, p)
10: eval(expr, p)
11: eval.parent(substitute(eval(quote(expr), envir)))
12: local(environment(), sapply(vars, get, envir = e, simplify = FALSE))
13: .lgc_evalmode$extract(fun(...))
14: (function (...) .lgc_evalmode$extract(fun(...)))(`AR1(x)` = 0.5)
15: do.call(object@fun, as.list(reparam(par)))
16: fun(...)
17: FUN(X[[i]], ...)
18: lapply(X = X, FUN = FUN, ...)
19: sapply(vars, get, envir = e, simplify = FALSE)
20: eval(quote(environment()), sapply(vars, get, envir = e, simplify = FALSE))
21: eval(expr, p)
22: eval(expr, p)
23: eval.parent(substitute(eval(quote(expr), envir)))
24: local(environment(), sapply(vars, get, envir = e, simplify = FALSE))
25: .lgc_evalmode$extract(fun(...))
26: X@fun(...)
27: fun(...)
28: FUN(X[[i]], ...)
29: lapply(X = X, FUN = FUN, ...)
30: sapply(vars, get, envir = e, simplify = FALSE)
31: eval(quote(environment()), sapply(vars, get, envir = e, simplify = FALSE))
32: eval(expr, p)
33: eval(expr, p)
34: eval.parent(substitute(eval(quote(expr), envir)))
35: local(environment(), sapply(vars, get, envir = e, simplify = FALSE))
36: .lgc_evalmode$extract(fun(...))
37: x@fun(...)
38: FUN(X[[i]], ...)
39: lapply(args, function(x) x@fun(...))
40: fun(...)
41: FUN(X[[i]], ...)
42: lapply(X = X, FUN = FUN, ...)
43: sapply(vars, get, envir = e, simplify = FALSE)
44: eval(quote(environment()), sapply(vars, get, envir = e, simplify = FALSE))
45: eval(expr, p)
46: eval(expr, p)
47: eval.parent(substitute(eval(quote(expr), envir)))
48: local(environment(), sapply(vars, get, envir = e, simplify = FALSE))
49: .lgc_evalmode$extract(fun(...))
50: X@fun(...)
51: fun(...)
52: FUN(X[[i]], ...)
53: lapply(X = X, FUN = FUN, ...)
54: sapply(vars, get, envir = e, simplify = FALSE)
55: eval(quote(environment()), sapply(vars, get, envir = e, simplify = FALSE))
56: eval(expr, p)
57: eval(expr, p)
58: eval.parent(substitute(eval(quote(expr), envir)))
59: local(environment(), sapply(vars, get, envir = e, simplify = FALSE))
60: .lgc_evalmode$extract(fun(...))
61: (function (...) .lgc_evalmode$extract(fun(...)))(`transf.AR1(x)` = 0.549306144334055, `transf.AR1(y)` = 0.549306144334055, `corr.AR2(y)1` = 0.0333333333333333, `AR2(y)2` = -0.5, lognugget. = 0)
62: do.call(x@fun, as.list(y))
63: evaluate(object)
64: .class1(object)
65: as(evaluate(object), "dsCMatrix")
66: simulate(C)
67: simulate(C)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 7 WARNINGs, 6 NOTEs
See
'/00check.log'
for details.


Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Windows 7 (R 3.0.x)

(lgc 1.4)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'lgc' ...
** libs

*** arch - i386
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chol.c -o chol.o
chol.c: In function 'kronecker_parallel':
chol.c:93:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c: In function 'inner_prod':
chol.c:111:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c:112:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c: In function 'chol':
chol.c:202:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
chol.c: In function 'inv':
chol.c:357:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:331:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:328:11: warning: unused variable 'k' [-Wunused-variable]
chol.c: In function 'recursion':
chol.c:414:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:416:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:438:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:458:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:400:46: warning: unused variable 'Li' [-Wunused-variable]
chol.c: In function 'inv_up':
chol.c:531:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:537:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
chol.c:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:516:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:516:16: warning: unused variable 'Lii' [-Wunused-variable]
chol.c:516:10: warning: unused variable 'sigij' [-Wunused-variable]
chol.c:515:21: warning: unused variable 'Sigmax' [-Wunused-variable]
chol.c:515:11: warning: unused variable 'Lx' [-Wunused-variable]
chol.c:514:46: warning: unused variable 'Sigmap' [-Wunused-variable]
chol.c:514:28: warning: unused variable 'Sigmai' [-Wunused-variable]
chol.c:514:18: warning: unused variable 'Lp' [-Wunused-variable]
chol.c:514:8: warning: unused variable 'Li' [-Wunused-variable]
chol.c:513:18: warning: unused variable 'nL0' [-Wunused-variable]
chol.c:513:15: warning: unused variable 'pt' [-Wunused-variable]
chol.c:513:11: warning: unused variable 'k' [-Wunused-variable]
chol.c:513:9: warning: unused variable 'j' [-Wunused-variable]
chol.c: At top level:
chol.c:183:12: warning: 'cs_diag' defined but not used [-Wunused-function]
chol.c: In function 'recursion':
chol.c:430:11: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
chol.c:398:6: warning: 'p' may be used uninitialized in this function [-Wuninitialized]
chol.c: In function 'inv_up':
chol.c:442:3: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
chol.c:400:59: note: 'pdiag' was declared here
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dist.c -o dist.o
dist.c: In function 'distkm':
dist.c:37:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
dist.c: In function 'nearestkm':
dist.c:56:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c lgc_sparse.c -o lgc_sparse.o
lgc_sparse.c: In function 'lgc_newton':
lgc_sparse.c:402:3: warning: suggest parentheses around operand of '!' or change '|' to '||' or '!' to '~' [-Wparentheses]
lgc_sparse.c:390:28: warning: variable 'Hp' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:13: warning: variable 'Hi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:8: warning: variable 'Qi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:388:10: warning: variable 'mgc_previous' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:387:27: warning: unused variable 'zero' [-Wunused-variable]
lgc_sparse.c:381:22: warning: unused variable 'mgc2' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_gradient':
lgc_sparse.c:562:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:572:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:575:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:588:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:550:7: warning: unused variable 'ndata' [-Wunused-variable]
lgc_sparse.c:549:8: warning: unused variable 'dataindex' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inner_prod':
lgc_sparse.c:703:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c:704:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:839:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:841:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:863:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:883:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:825:46: warning: unused variable 'Li' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inv_up':
lgc_sparse.c:929:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c: In function 'lgc_recursion_super':
lgc_sparse.c:1035:8: warning: unused variable 'p' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_recursion.constprop.0':
lgc_sparse.c:867:3: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:855:11: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
lgc_sparse.c:823:6: warning: 'p' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c local_stubs.c -o local_stubs.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ops.c -o ops.o
ops.c: In function 'mul_sparse':
ops.c:67:72: warning: unused variable 'Bnzmax' [-Wunused-variable]
ops.c:67:43: warning: unused variable 'Bn' [-Wunused-variable]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c winfix.c -o winfix.o
gcc -m32 -shared -s -static-libgcc -o lgc.dll tmp.def chol.o dist.o lgc_sparse.o local_stubs.o ops.o winfix.o C:/PROGRA~1/r/r-3.0/library/Matrix/libs//i386/Matrix.dll -LC:/PROGRA~1/r/r-3.0/bin/i386 -lRlapack -LC:/PROGRA~1/r/r-3.0/bin/i386 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/i386 -lR
installing to z:/rforge/Rlib/win7-3.0/lgc/libs/i386

*** arch - x64
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chol.c -o chol.o
chol.c: In function 'kronecker_parallel':
chol.c:93:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c: In function 'inner_prod':
chol.c:111:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c:112:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c: In function 'chol':
chol.c:202:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
chol.c: In function 'inv':
chol.c:357:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:331:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:328:11: warning: unused variable 'k' [-Wunused-variable]
chol.c: In function 'recursion':
chol.c:414:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:416:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:438:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:458:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:400:46: warning: unused variable 'Li' [-Wunused-variable]
chol.c: In function 'inv_up':
chol.c:531:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:537:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
chol.c:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:516:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:516:16: warning: unused variable 'Lii' [-Wunused-variable]
chol.c:516:10: warning: unused variable 'sigij' [-Wunused-variable]
chol.c:515:21: warning: unused variable 'Sigmax' [-Wunused-variable]
chol.c:515:11: warning: unused variable 'Lx' [-Wunused-variable]
chol.c:514:46: warning: unused variable 'Sigmap' [-Wunused-variable]
chol.c:514:28: warning: unused variable 'Sigmai' [-Wunused-variable]
chol.c:514:18: warning: unused variable 'Lp' [-Wunused-variable]
chol.c:514:8: warning: unused variable 'Li' [-Wunused-variable]
chol.c:513:18: warning: unused variable 'nL0' [-Wunused-variable]
chol.c:513:15: warning: unused variable 'pt' [-Wunused-variable]
chol.c:513:11: warning: unused variable 'k' [-Wunused-variable]
chol.c:513:9: warning: unused variable 'j' [-Wunused-variable]
chol.c: At top level:
chol.c:183:12: warning: 'cs_diag' defined but not used [-Wunused-function]
chol.c: In function 'recursion':
chol.c:398:6: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dist.c -o dist.o
dist.c: In function 'distkm':
dist.c:37:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
dist.c: In function 'nearestkm':
dist.c:56:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c lgc_sparse.c -o lgc_sparse.o
lgc_sparse.c: In function 'lgc_newton':
lgc_sparse.c:402:3: warning: suggest parentheses around operand of '!' or change '|' to '||' or '!' to '~' [-Wparentheses]
lgc_sparse.c:390:28: warning: variable 'Hp' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:13: warning: variable 'Hi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:8: warning: variable 'Qi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:388:10: warning: variable 'mgc_previous' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:387:27: warning: unused variable 'zero' [-Wunused-variable]
lgc_sparse.c:381:22: warning: unused variable 'mgc2' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_gradient':
lgc_sparse.c:562:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:572:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:575:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:588:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:550:7: warning: unused variable 'ndata' [-Wunused-variable]
lgc_sparse.c:549:8: warning: unused variable 'dataindex' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inner_prod':
lgc_sparse.c:703:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c:704:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:839:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:841:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:863:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:883:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:825:46: warning: unused variable 'Li' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inv_up':
lgc_sparse.c:929:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c: In function 'lgc_recursion_super':
lgc_sparse.c:1035:8: warning: unused variable 'p' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:823:6: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c local_stubs.c -o local_stubs.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ops.c -o ops.o
ops.c: In function 'mul_sparse':
ops.c:67:72: warning: unused variable 'Bnzmax' [-Wunused-variable]
ops.c:67:43: warning: unused variable 'Bn' [-Wunused-variable]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c winfix.c -o winfix.o
gcc -m64 -shared -s -static-libgcc -o lgc.dll tmp.def chol.o dist.o lgc_sparse.o local_stubs.o ops.o winfix.o C:/PROGRA~1/r/r-3.0/library/Matrix/libs//x64/Matrix.dll -LC:/PROGRA~1/r/r-3.0/bin/x64 -lRlapack -LC:/PROGRA~1/r/r-3.0/bin/x64 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/x64 -lR
installing to z:/rforge/Rlib/win7-3.0/lgc/libs/x64
** R
** data
** demo
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'lgc'
Creating a generic function for 'simulate' from package 'stats' in package 'lgc'
Warning: in method for 'coerce' with signature '"gridFactor","distFactor"': no definition for classes "gridFactor", "distFactor"
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: ignoring .First.lib() for package 'lgc'
*** arch - x64
Warning: ignoring .First.lib() for package 'lgc'
* MD5 sums
packaged installation of 'lgc' as lgc_1.4.zip
* DONE (lgc)