[R] R check passes code and docs that don't match

Ross Boylan ross at biostat.ucsf.edu
Fri Nov 5 20:16:22 CET 2004

I have code and documentation that don't match, but R CMD check didn't
flag it.

in mspath.R
mspath <- function(formula,   # formula with  observed Markov states  
~  observation times (required)
                qmatrix,    # matrix of 1s and 0s with indices of
allowed transitions (diagonal is ignored) (required)
                misc = FALSE,
                ematrix = NULL,    # matrix of 1s and 0s with indices of
allowed misclassfications (diagonal is ignored) (required)
                inits,      # initial values of optimisation or fixed
values (required)
                subject = NULL, # optional, defaults to all the same if
not given
                covariates = NULL, # formula specifying covariates on
transition rates.
                constraint = NULL, # which intensities have covariates
on them (as in Marshall et al.)
                misccovariates = NULL, # formula specifying covariates
on misclassification probs
                miscconstraint = NULL, # which misc probs have
covariates on them
                qconstraint = NULL, # constraints on equality of
baseline intensities
                econstraint = NULL, # constraints on equality of
baseline misc probs
                covmatch = "previous",   # take the covariate value from
the previous or next observation
                initprobs = NULL,  # initial state occupancy
                data=list(),       # optional data frame in which to
interpret variable names
                fromto = FALSE,
                fromstate, #
                tostate,   #  data required if fromto is TRUE
                timelag,   #
                death = FALSE,  # 'death' states, ie, entry time known
exactly, but unknown transient state at previous instant
                tunit = 1.0, # no longer used
                exacttimes = FALSE,
                fixedpars = NULL, # specify which parameters to fix
                stepnumerator = 1,  # maximum step size in discrete
                stepdenominator = 1,  # rational number; use integers
                do.what = 1, # 1 for likelihood, 0 for counts
                ... # options to optim

in mspath.Rd
mspath ( formula, qmatrix, misc = FALSE, ematrix, inits, subject,
      covariates = NULL, constraint = NULL, misccovariates = NULL,
      miscconstraint = NULL, qconstraint=NULL, econstraint=NULL,
      covmatch = "previous", initprobs = NULL, 
      data = list(), fromto = FALSE, fromstate, tostate, timelag,
      death = FALSE, tunit = 1.0, exacttimes = FALSE,
      fixedpars = NULL, stepsize=1.0... )
with corresponding \item's in the \arguments list.

Among the differences (see the end of the argument lists)
In code by not Rd: stepnumerator, stepdenominator, do.what
In Rd but not code: stepsize

Yet R CMD check says
** help
 >>> Building/Updating help pages for package 'mspath'
     Formats: text html latex example 
  mspath                            text    html    latex
     missing link(s):  qmatrix.mspath ematrix.mspath simmulti.mspath
print.mspath plot.mspath summary.mspath qmatrix.mspath pmatrix.mspath
* DONE (mspath)

* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  MatrixExp absorbing.mspath coef.mspath crudeinits.mspath deltamethod
  ematrix.mspath expit expitsum expsum hazard.mspath lik.mspath logit
  mspath.check.consistency mspath.check.ematrix mspath.check.model
  mspath.check.qmatrix mspath.check.state mspath.check.times
  mspath.form.output mspath.process.covs mspath.results
  observed.mspath odds.mspath plot.mspath pmatrix.mspath
  pmatrix.piecewise.mspath prevalence.mspath print.mspath
  print.summary.mspath qematrix.diagse.formstr qematrix.diagse.mspath
  qematrix.mspath qmatrix.mspath qratio.mspath qratio.se.mspath
  sojourn.mspath statetable.mspath summary.mspath totlos.mspath
  transient.mspath viterbi.mspath
Undocumented data sets:
  e2 gold q2
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK

Have I misunderstood how this is suppsed to work?  Have the previous
errors confused or voided the code/documentation test?  Is it a bug?

Using R 2.0.0-3 on Debian.
Ross Boylan                                      wk:  (415) 502-4031
530 Parnassus Avenue (Library) rm 115-4          ross at biostat.ucsf.edu
Dept of Epidemiology and Biostatistics           fax: (415) 476-9856
University of California, San Francisco
San Francisco, CA 94143-0840                     hm:  (415) 550-1062

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