- using R Under development (unstable) (2012-02-27 r58511)
- using platform: x86_64-pc-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'depmix/DESCRIPTION' ... OK
- this is package 'depmix' version '0.9.10'
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: 'Rdonlp2'
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking whether package 'depmix' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level 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
- loading checks for arch 'i386'
** 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
- loading checks for arch 'x64'
** 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 for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... NOTE
bootstrap: warning in generate(dmm = mod, nt = ntimes(dat)): partial
argument match of 'nt' to 'ntimes'
bootstrap: warning in loglike(dat = gen, dmm = mod, print = 0): partial
argument match of 'print' to 'printlevel'
bootstrap: warning in fitdmm(dat = gen, dmm = mod, print = 0, ses = 0,
postst = 0, poster = FALSE): partial argument match of 'print' to
'printlevel'
checkSetRecode: warning in markovdata(dat = dat[[i]][, (nrit +
1):(dim(dat[[i]])[2]), drop = FALSE], itemt = itt, nt =
ntimes(dat[[i]])): partial argument match of 'itemt' to 'itemtypes'
checkSetRecode: warning in markovdata(dat = dat[[i]][, (nrit +
1):(dim(dat[[i]])[2]), drop = FALSE], itemt = itt, nt =
ntimes(dat[[i]])): partial argument match of 'nt' to 'ntimes'
checkSetRecode: warning in markovdata(dat = dat[[i]][, 1:nrit, drop =
FALSE], itemtypes = itemtypes(dat[[i]])[1:nrit], nt =
ntimes(dat[[i]]), replicates = replicates(dat[[i]])): partial
argument match of 'nt' to 'ntimes'
computeSes: warning in loglike(dat = dat, dmm = mod, grad = TRUE, tdcov
= 0, print = 0): partial argument match of 'print' to 'printlevel'
computeSes: warning in loglike(dat = dat, dmm = mod, grad = TRUE, hess
= FALSE, set = FALSE, tdcov = 0, print = 0): partial argument match
of 'print' to 'printlevel'
computeSes: warning in matrix(mod$A[, which(mod$fixed[1:mod$npars] ==
1)], nr = nrow(mod$A)): partial argument match of 'nr' to 'nrow'
dmm: warning in matrix(stval[2:(nstates * nstates + 1)], nr = nstates,
byrow = TRUE): partial argument match of 'nr' to 'nrow'
dmm: warning in matrix(stval[(nstates * nstates + 2):(npars -
nstates)], nr = nstates, byrow = TRUE): partial argument match of
'nr' to 'nrow'
dmm: warning in matrix(runif(nstates * nstates, 0, 1), nr = nstates):
partial argument match of 'nr' to 'nrow'
dmm: warning in matrix(0, nr = nstates, nc = sum(lobs)): partial
argument match of 'nr' to 'nrow'
dmm: warning in matrix(0, nr = nstates, nc = sum(lobs)): partial
argument match of 'nc' to 'ncol'
dmm: warning in paridx(nstates, itemtypes, m = "ob", idx1 = j, it = i):
partial argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "tr", i): partial
argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "ob", it = j, idx1 = i):
partial argument match of 'm' to 'mat'
dmm: warning in matrix(conrows, nc = npars, byrow = TRUE): partial
argument match of 'nc' to 'ncol'
dmm: warning in paridx(nstates, itemtypes, m = "tr"): partial argument
match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "ob"): partial argument
match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "in"): partial argument
match of 'm' to 'mat'
dmm: warning in matrix(tdpars[paridx(nstates, itemtypes, m = "tr")], nr
= nstates, byrow = TRUE): partial argument match of 'nr' to 'nrow'
dmm: warning in paridx(nstates, itemtypes, m = "tr", idx1 = i): partial
argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "tr", idx1 = i, idx2 =
j): partial argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "ob", idx1 = i, it = j):
partial argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "ob", idx1 = i, it = j,
idx2 = k): partial argument match of 'm' to 'mat'
dmm: warning in paridx(nstates, itemtypes, m = "in", idx1 = i): partial
argument match of 'm' to 'mat'
dmm: warning in matrix(as.logical(A), nr = nrow(A)): partial argument
match of 'nr' to 'nrow'
fitdmm: warning in loglike(dat = dat, dmm = xgmod, tdcov = tdcov, print
= 0, set = FALSE): partial argument match of 'print' to 'printlevel'
fitdmm: warning in matrix(as.logical(A), nr = nrow(A)): partial
argument match of 'nr' to 'nrow'
fitdmm : logl: warning in loglike(dat = dat, dmm = xgmod, print = 0,
set = FALSE, tdcov = tdcov): partial argument match of 'print' to
'printlevel'
fitdmm : grad: warning in loglike(dat = dat, dmm = xgmod, print = 0,
set = FALSE, tdcov = tdcov, grad = TRUE): partial argument match of
'print' to 'printlevel'
fitdmm: no visible global function definition for 'donlp2'
fitdmm: no visible global function definition for 'donlp2.control'
fitdmm: warning in matrix(bulin, nc = 1): partial argument match of
'nc' to 'ncol'
fitdmm: warning in matrix(xgmod$bllin[idx], nc = 1): partial argument
match of 'nc' to 'ncol'
fitdmm: warning in matrix(xgmod$bulin[idx], nc = 1): partial argument
match of 'nc' to 'ncol'
fitdmm : f: warning in loglike(dat = dat, dmm = xgmod, print = 0, set =
FALSE, tdcov = tdcov): partial argument match of 'print' to
'printlevel'
fitdmm : f: no visible binding for global variable 'fcalls'
fitdmm : gr: warning in loglike(dat = dat, dmm = xgmod, grad = TRUE,
print = 0, set = FALSE): partial argument match of 'print' to
'printlevel'
fitdmm : gr: no visible binding for global variable 'fcalls'
fitdmm: no visible binding for global variable 'totalviolation'
fitdmm : f: warning in loglike(dat = dat, dmm = xgmod, print = 0, grad
= TRUE, set = FALSE): partial argument match of 'print' to
'printlevel'
fitdmm : f: warning in loglike(dat = dat, dmm = xgmod, tdcov = tdcov,
print = 0, grad = FALSE, set = FALSE): partial argument match of
'print' to 'printlevel'
fitdmm: no visible binding for global variable 'loglvalue'
generate: warning in paridx(dmm$nstates, dmm$itemtypes, m = "tr", comp
= i): partial argument match of 'm' to 'mat'
generate: warning in paridx(dmm$nstates, dmm$itemtypes, m = "ob", comp
= i): partial argument match of 'm' to 'mat'
generate: warning in paridx(dmm$nstates, dmm$itemtypes, m = "in", comp
= i): partial argument match of 'm' to 'mat'
generate: warning in matrix(0, nc = nitems, nr = sum(ntimes)): partial
argument match of 'nr' to 'nrow'
generate: warning in matrix(0, nc = nitems, nr = sum(ntimes)): partial
argument match of 'nc' to 'ncol'
generate: warning in markovdata(dat = obs, itemt = dmm$itemtnames,
ntimes = ntimes): partial argument match of 'itemt' to 'itemtypes'
lca: warning in matrix(conrows, nc = lcmnp, byrow = TRUE): partial
argument match of 'nc' to 'ncol'
lca: warning in matrix(0, nr = nrow(conrows), nc = nclasses *
nclasses): partial argument match of 'nr' to 'nrow'
lca: warning in matrix(0, nr = nrow(conrows), nc = nclasses *
nclasses): partial argument match of 'nc' to 'ncol'
lca: warning in matrix(0, nr = nrow(linmat), nc = nclasses * nclasses):
partial argument match of 'nr' to 'nrow'
lca: warning in matrix(0, nr = nrow(linmat), nc = nclasses * nclasses):
partial argument match of 'nc' to 'ncol'
mgdmm: warning in paridx(nstates, itemtypes, comp = i, m = "tr"):
partial argument match of 'm' to 'mat'
mgdmm: warning in paridx(nstates, itemtypes, comp = i, m = "ob"):
partial argument match of 'm' to 'mat'
mgdmm: warning in paridx(nstates, itemtypes, comp = i, m = "in"):
partial argument match of 'm' to 'mat'
mgdmm: warning in matrix(A[idx, ], nc = nparstotal): partial argument
match of 'nc' to 'ncol'
mixdmm: warning in matrix(rep(1, nrcomp), nr = 1): partial argument
match of 'nr' to 'nrow'
mixdmm: warning in matrix(conrows, nc = npars, byrow = TRUE): partial
argument match of 'nc' to 'ncol'
mixdmm: warning in matrix(0, nc = npars, nr = nr): partial argument
match of 'nr' to 'nrow'
mixdmm: warning in matrix(0, nc = npars, nr = nr): partial argument
match of 'nc' to 'ncol'
posterior: warning in matrix(0, nc = (2 + sum(xgmod$nstates)), nr = 0):
partial argument match of 'nr' to 'nrow'
posterior: warning in matrix(0, nc = (2 + sum(xgmod$nstates)), nr = 0):
partial argument match of 'nc' to 'ncol'
posterior: warning in matrix(c(rep(z$postcomp, ntimes(dat[[g]])[i]),
z$states, matrix(z$postdelta, nc = sum(xgmod$nstates), byrow =
TRUE)), nc = (2 + sum(xgmod$nstates))): partial argument match of
'nc' to 'ncol'
posterior: warning in matrix(z$postdelta, nc = sum(xgmod$nstates),
byrow = TRUE): partial argument match of 'nc' to 'ncol'
summary.dmm: warning in paridx(object$nstates, object$itemtypes, m =
"tr"): partial argument match of 'm' to 'mat'
summary.dmm: warning in paridx(object$nstates, object$itemtypes, m =
"ob"): partial argument match of 'm' to 'mat'
summary.dmm: warning in matrix(0, object$nstates * 3, nc = ncol(obsx)):
partial argument match of 'nc' to 'ncol'
summary.dmm: warning in paridx(object$nstates, object$itemtypes, m =
"in"): partial argument match of 'm' to 'mat'
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... NOTE
File 'd:/Rcompile/CRANpkg/lib/2.15/depmix/libs/i386/depmix.dll':
Found 'abort', possibly from 'abort' (C)
File 'd:/Rcompile/CRANpkg/lib/2.15/depmix/libs/x64/depmix.dll':
Found 'abort', possibly from 'abort' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
- checking sizes of PDF files under 'inst/doc' ... OK
- checking installed files from 'inst/doc' ... OK
- checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
- checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
'd:/Rcompile/CRANpkg/local/2.15/depmix.Rcheck/00check.log'
for details.