• using R version 3.0.1 Patched (2013-05-18 r62762)
• using platform: sparc-sun-solaris2.10 (32-bit)
• using session charset: UTF-8
• 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 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 whether package ‘depmix’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• 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 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: 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 : gr: warning in loglike(dat = dat, dmm = xgmod, grad = TRUE,
  print = 0, set = FALSE): partial argument match of 'print' to
  'printlevel'
  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'
  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'
  fitdmm: no visible global function definition for ‘donlp2’
  fitdmm: no visible global function definition for ‘donlp2.control’
  fitdmm : f: no visible binding for global variable ‘fcalls’
  fitdmm : gr: no visible binding for global variable ‘fcalls’
  fitdmm: no visible binding for global variable ‘totalviolation’
  fitdmm: no visible binding for global variable ‘loglvalue’
• 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 ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [381s/381s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/ripley/R/packages/tests32/depmix.Rcheck/00check.log’
  for details.