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cthmm log file (check_x86_64_linux)

Mon Jul 21 22:15:29 2014: Checking package cthmm (SVN revision 24) ...
* using log directory ‘/mnt/building/build_2014-07-21-22-06/RF_PKG_CHECK/PKGS/cthmm.Rcheck’
* using R version 3.1.1 Patched (2014-07-20 r66218)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘cthmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cthmm’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Jane Lange ’
New submission
Non-FOSS package license (GSL)
Vignette sources in 'inst/doc' with no 'vignettes' directory:
  ‘manual.Rnw’
A 'vignettes' directory is required as from R 3.1.0
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped

Depends: includes the non-default packages:
  ‘Rcpp’ ‘RcppArmadillo’ ‘msm’ ‘SQUAREM’ ‘magic’ ‘numDeriv’ ‘corpcor’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
* 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 ‘cthmm’ can be installed ... [120s/122s] OK
* checking installed package size ... NOTE
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  GSL
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Empty or missing file ‘demo/00Index’.
See the information on INDEX files and package subdirectories in the
chapter ‘Creating R packages’ of the ‘Writing R Extensions’ manual.
* 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
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘SQUAREM’ ‘corpcor’ ‘magic’ ‘msm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
update:
  function(object, ...)
update.emission.params:
  function(current.params, emission.setup, emission.counts, max.it)

update:
  function(object, ...)
update.init.params:
  function(current.params, init.setup, init.counts, max.it)

update:
  function(object, ...)
update.multinom.params:
  function(current.params, covariate.array, deriv.array, param.types,
           counts, N_vector, max.it, no.NR)

update:
  function(object, ...)
update.rate.params:
  function(current.params, rate.setup, transitions, durations, max.it)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'get.init.matrix.list.Rd':
  \examples lines wider than 100 characters:
     init.list=get.init.matrix.list(current.params=fit.4state$params[12:13],init.setup=init.setup,do.list=T)

Rd file 'sub_dist_times.Rd':
  \examples lines wider than 100 characters:
          main="Cumulative distribution function for first passage time from state A to B, for covariate X=0")

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘E_step_DDO’ ‘E_step_emission_init_all’
  ‘E_step_emission_init_all_time_dep’ ‘NR_update’
  ‘cappe.first.moment.tau’ ‘cappe.second.moment.tau’ ‘delta.method.mat’
  ‘dens.fun.deriv’ ‘dens.fun.deriv.single’ ‘dist.fun’ ‘dist.fun.deriv’
  ‘dur_loop_R’ ‘dur_times_R’ ‘eigen_decomp_list_R’
  ‘emission.score.hessian’ ‘emission.score.hessian.old’ ‘extract_array’
  ‘extract_mat’ ‘fill.variables’ ‘forward_modified’ ‘forwardback_R’
  ‘get.emission.init.states’ ‘get.prob.array’ ‘get.rates’ ‘get_LL’
  ‘get_density’ ‘get_hazard’ ‘get_mean’ ‘get_sub_distribution’
  ‘haz.fun.deriv’ ‘haz.fun.deriv.single’ ‘joint_dur_dur_times’
  ‘joint_dur_trans_times’ ‘joint_mean_markov_jumps’
  ‘joint_mean_markov_rewards’ ‘joint_trans_trans_times’ ‘mat.exp’
  ‘mat.exp.deriv’ ‘mat_exp’ ‘mat_exp_eigen_R’
  ‘multinom.covariance.array’ ‘multinom.hessian’ ‘multinom.score’
  ‘multinom.score.old’ ‘populate_emission_matrix’
  ‘populate_initial_dist’ ‘populate_rate_matrix’ ‘rate.deriv’
  ‘rate_hessian’ ‘rate_score’ ‘s_2’ ‘se.dens.times’ ‘t1_2’
  ‘trans_loop_R’ ‘trans_probs_all’ ‘trans_times_R’
  ‘transition_prob_list’ ‘transition_probs’ ‘uniformization_mean’
  ‘update.multinom.params’
Undocumented data sets:
  ‘.Random.seed’ ‘DDO.setup’ ‘DDO_EM’ ‘DDO_data’ ‘cov.data’
  ‘covariance_DDO’ ‘design’ ‘design.matrix’ ‘emission.setup’
  ‘init.setup’ ‘out’ ‘rates.setup’ ‘returnlist’ ‘covariance_4state’
  ‘design.emission’ ‘design.init’ ‘design.matrix.init’ ‘fit.4state’
  ‘start’ ‘the.data’ ‘time’
All user-level objects in a package should have documentation entries.
See the 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 'E.step.emission.init.all'
  ‘num.obs.states’
Documented arguments not in \usage in documentation object 'E.step.emission.init.all':
  ‘num.obs.state’

Undocumented arguments in documentation object 'EM'
  ‘maxiter’
Documented arguments not in \usage in documentation object 'EM':
  ‘maxiter=500’

Duplicated \argument entries in documentation object 'emission_hessian_louis':
  ‘emission.setup’ ‘param.values’ ‘emission.counts’

Undocumented arguments in documentation object 'get_M1_M2_list'
  ‘transition.probabilties.list’
Documented arguments not in \usage in documentation object 'get_M1_M2_list':
  ‘transition.probabilities.list’

Undocumented arguments in documentation object 'get_variance'
  ‘absorb.state’

Duplicated \argument entries in documentation object 'init_hessian_louis':
  ‘init.setup’ ‘param.values’

Undocumented arguments in documentation object 'init_score_louis'
  ‘param.values’
Documented arguments not in \usage in documentation object 'init_score_louis':
  ‘init.param.values’

Undocumented arguments in documentation object 'louis_information'
  ‘delta.list’ ‘init.counts’ ‘transitions’
Documented arguments not in \usage in documentation object 'louis_information':
  ‘init.list’

Duplicated \argument entries in documentation object 'rate_hessian_louis':
  ‘rates.setup’ ‘rate.param.values’ ‘durations’

Duplicated \argument entries in documentation object 'rate_score_louis':
  ‘rates.setup’ ‘rate.param.values’ ‘durations’ ‘transitions’

Undocumented arguments in documentation object 's_1'
  ‘rate_eigen’ ‘exact_time_ranks’ ‘absorb_state’

Undocumented arguments in documentation object 's_1_oij'
  ‘num_states’

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 the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'update.emission.params':
  ‘update.emission.params’

S3 methods shown with full name in documentation object 'update.init.params':
  ‘update.init.params’

S3 methods shown with full name in documentation object 'update.rate.params':
  ‘update.rate.params’

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

Argument items with no description in Rd object 'construct.init.setup':
  ‘deriv.array’

Argument items with no description in Rd object 'construct.rates.setup':
  ‘deriv.array’

Argument items with no description in Rd object 'get.deriv.array':
  ‘covariate.array’

Argument items with no description in Rd object 's_1_Ni':
  ‘num_states’ ‘num_times’

Argument items with no description in Rd object 's_1_di':
  ‘num_states’ ‘time_diffs’ ‘rate_eigen’ ‘exact_time_ranks’
  ‘absorb_state’

Argument items with no description in Rd object 's_1_nij':
  ‘ni’ ‘nj’ ‘exact_time_ranks’ ‘absorb_state’ ‘rate_eigen’

Argument items with no description in Rd object 's_1_oij':
  ‘obs_data’ ‘num_times’

Argument items with no description in Rd object 's_1_zi':
  ‘num_states’ ‘num_times’

Argument items with no description in Rd object 't1_1_Ni':
  ‘Ni’ ‘num_states’

Argument items with no description in Rd object 't1_1_oij':
  ‘oi’ ‘oj’ ‘num_states’ ‘obs_data’

Argument items with no description in Rd object 't1_1_zi':
  ‘num_states’ ‘zi’

* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘manual.pdf’ from 515Kb to 218Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘manual.Rnw’
A ‘vignettes’ directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ... [3s/3s] OK
* checking PDF version of manual ... OK

WARNING: There were 7 warnings.
NOTE: There were 6 notes.
See
  ‘/mnt/building/build_2014-07-21-22-06/RF_PKG_CHECK/PKGS/cthmm.Rcheck/00check.log’
for details.

Run time: 196.8 seconds.