Fresh .r, .rd, DESCRIPTION, NAMESPACE: 1 error | 7 warnings | 2 notes

[swihart]

NO MORE ROXYGEN / DEVTOOLS::DOCUMENT() FOR event

==> devtools::check(document = FALSE)

Setting env vars ---------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building event -----------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build '/Users/swihartbj/github/event'  \
  --no-resave-data --no-manual 

* checking for file ‘/Users/swihartbj/github/event/DESCRIPTION’ ... OK
* preparing ‘event’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether ‘INDEX’ is up-to-date ... NO
* use ‘--force’ to remove the existing ‘INDEX’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘event/README_files/figure-html’
Removed empty directory ‘event/README_files’
* building ‘event_1.1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking event -----------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  '/var/folders/tv/9xflkyxs21j3747s8wd641t1bd7ntf/T//RtmpEX5Q15/event_1.1.0.tar.gz'  \
  --as-cran --timings --no-manual 

* using log directory ‘/Users/swihartbj/github/event.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘event/DESCRIPTION’ ... OK
* this is package ‘event’ version ‘1.1.0’
* package encoding: UTF-8
* 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 whether package ‘event’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Rank mismatch in argument 'valrho' at (1) (rank-1 and scalar)
See ‘/Users/swihartbj/github/event.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
baseline:
  function(z, ...)
baseline.survivalkit:
  function(z)

plot.dist:
  function(z, ...)
plot.dist.km:
  function(z)

plot.intensity:
  function(z, ...)
plot.intensity.default:
  function(times, censor, group, colour, mix, ylim, ylab, xlab, main)

survival:
  function(z, ...)
survival.survivalkit:
  function(z)

print:
  function(x, ...)
print.intensity:
  function(z)

print:
  function(x, ...)
print.kalsurv:
  function(z, digits, correlation)

print:
  function(x, ...)
print.km:
  function(z)

print:
  function(x, ...)
print.llrf:
  function(z)

print:
  function(x, ...)
print.pbirth:
  function(z)

print:
  function(x, ...)
print.survivalkit:
  function(z)

plot:
  function(x, ...)
plot.dist:
  function(z, ...)

plot:
  function(x, ...)
plot.dist.km:
  function(z)

plot:
  function(x, ...)
plot.intensity:
  function(z, ...)

plot:
  function(x, ...)
plot.intensity.default:
  function(times, censor, group, colour, mix, ylim, ylab, xlab, main)

plot:
  function(x, ...)
plot.intensity.km:
  function(z, add, xlab, ylab, type, lty, ...)

plot:
  function(x, ...)
plot.km:
  function(z, add, xlim, ylim, main, xlab, ylab, lty, ...)

plot:
  function(x, ...)
plot.surv:
  function(times, survivor, group, cdf, add, xlim, ylim, main, xlab,
           ylab, lty, ...)

deviance:
  function(object, ...)
deviance.intensity:
  function(z)

deviance:
  function(object, ...)
deviance.kalsurv:
  function(z)

deviance:
  function(object, ...)
deviance.pbirth:
  function(z)

fitted:
  function(object, ...)
fitted.kalsurv:
  function(z, recursive)

residuals:
  function(object, ...)
residuals.kalsurv:
  function(z, recursive)

residuals:
  function(object, ...)
residuals.survivalkit:
  function(z)

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

Found the following apparent S3 methods exported but not registered:
  baseline.survivalkit deviance.intensity deviance.kalsurv
  deviance.pbirth fitted.kalsurv plot.dist plot.dist.km plot.dist.km
  plot.intensity plot.intensity.default plot.intensity.default
  plot.intensity.km plot.intensity.km plot.km plot.surv print.intensity
  print.kalsurv print.km print.llrf print.pbirth print.survivalkit
  residuals.kalsurv residuals.survivalkit survival.survivalkit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("ksurvg", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), distribution = as.integer(dst), 
       density = as.integer(density), dep = as.integer(dep), birth = as.integer(birth), 
       tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("frailb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), 
       tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(0), 
       pred = double(n), rpred = double(n), rf = as.integer(rf), 
       bb = as.double(b), sf = as.integer(sf), vv = as.double(v), 
       frser = as.integer(frser), like = double(1), DUP = FALSE, 
       PACKAGE = "event")
   .C("frailb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), 
       tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(1), 
       pred = double(n), rpred = double(n), rf = as.integer(rf), 
       bb = as.double(b), sf = as.integer(sf), vv = as.double(v), 
       frser = as.integer(frser), like = double(1), DUP = FALSE, 
       PACKAGE = "event")
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(1), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("ksurvg", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), distribution = as.integer(dst), 
       density = as.integer(density), dep = as.integer(dep), birth = as.integer(birth), 
       tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(1), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .Fortran("weibull", iconst = as.integer(iconst), rconst = as.double(rconst), 
       istime = as.integer(istime), squant = as.double(squant), 
       valrho = as.double(valrho), includ = as.integer(includ), 
       info = as.integer(info), itabl = as.integer(itabl), xtabl = as.double(xtabl), 
       nrr = as.integer(nrr), info2 = as.integer(info2), itabl2 = as.integer(itabl2), 
       xtabl2 = as.double(xtabl2), ipedig = as.integer(pedigree), 
       nrr2 = as.integer(nrr2), nccov = as.integer(nccov), ndcov = as.integer(ndcov), 
       nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), DUP = FALSE, 
       PACKAGE = "event")
   .Fortran("cox", iconst = as.integer(iconst), rconst = as.double(rconst), 
       istime = as.integer(istime), squant = as.double(squant), 
       includ = as.integer(includ), info = as.integer(info), itabl = as.integer(itabl), 
       xtabl = as.double(xtabl), nrr = as.integer(nrr), info2 = as.integer(info2), 
       itabl2 = as.integer(itabl2), xtabl2 = as.double(xtabl2), 
       iplus1 = as.integer(iplus1), iplus2 = as.integer(iplus2), 
       ipedig = as.integer(pedigree), nrr2 = as.integer(nrr2), nccov = as.integer(nccov), 
       ndcov = as.integer(ndcov), nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), km = double(nrr * 
           nstrata * 4), resid = double(nrr * nstrata * 3), ut = as.integer(nrr * 
           nstrata), DUP = FALSE, PACKAGE = "event")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

autointensity: no visible global function definition for ‘hist’
autointensity: no visible global function definition for ‘lines’
coxre : like: no visible global function definition for ‘glm’
coxre : like: no visible binding for global variable ‘poisson’
coxre : likel: no visible global function definition for ‘glm’
coxre : likel: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘glm’
coxre: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘nlm’
cprocess: no visible global function definition for ‘lines’
cprocess: no visible global function definition for ‘plot’
cprocess: no visible global function definition for ‘text’
ehr: no visible global function definition for ‘nlm’
hboxcox: no visible global function definition for ‘pnorm’
hcauchy: no visible global function definition for ‘dcauchy’
hcauchy: no visible global function definition for ‘pcauchy’
hgamma: no visible global function definition for ‘dgamma’
hgamma: no visible global function definition for ‘pgamma’
hgextval: no visible global function definition for ‘pweibull’
hggamma: no visible global function definition for ‘pgamma’
hinvgauss: no visible global function definition for ‘pnorm’
hlnorm: no visible global function definition for ‘dlnorm’
hlnorm: no visible global function definition for ‘plnorm’
hlogis: no visible global function definition for ‘dlogis’
hlogis: no visible global function definition for ‘plogis’
hnorm: no visible global function definition for ‘dnorm’
hnorm: no visible global function definition for ‘pnorm’
hstudent : pst: no visible global function definition for ‘pbeta’
kalsurv: no visible global function definition for ‘terms’
kalsurv : sh1: no visible binding for global variable ‘npl1’
kalsurv: no visible global function definition for ‘nlm’
pbirth: no visible global function definition for ‘nlm’
plot.dist.km: no visible global function definition for ‘par’
plot.dist.km: no visible global function definition for ‘plot’
plot.dist.km: no visible global function definition for ‘lines’
plot.dist.km: no visible global function definition for ‘qnorm’
plot.intensity.default: no visible global function definition for
  ‘plot’
plot.intensity.default: no visible global function definition for
  ‘lines’
plot.intensity.default: no visible global function definition for
  ‘gray’
plot.intensity.km: no visible global function definition for ‘lines’
plot.intensity.km: no visible global function definition for ‘plot’
plot.km: no visible global function definition for ‘lines’
plot.km: no visible global function definition for ‘plot’
plot.surv: no visible global function definition for ‘lines’
plot.surv: no visible global function definition for ‘plot’
survkit: no visible global function definition for ‘model.frame’
survkit: no visible global function definition for ‘terms’
survkit: no visible binding for global variable ‘na.fail’
Undefined global functions or variables:
  dcauchy dgamma dlnorm dlogis dnorm glm gray hist lines model.frame
  na.fail nlm npl1 par pbeta pcauchy pgamma plnorm plogis plot pnorm
  poisson pweibull qnorm terms text
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "hist", "lines", "par", "plot", "text")
  importFrom("stats", "dcauchy", "dgamma", "dlnorm", "dlogis", "dnorm",
             "glm", "model.frame", "na.fail", "nlm", "pbeta", "pcauchy",
             "pgamma", "plnorm", "plogis", "pnorm", "poisson",
             "pweibull", "qnorm", "terms")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) bp.Rd:0-32: Must have a \description
checkRd: (5) hcauchy.Rd:0-31: Must have a \description
checkRd: (5) hexp.Rd:0-30: Must have a \description
checkRd: (5) hgamma.Rd:0-32: Must have a \description
checkRd: (5) hlnorm.Rd:0-31: Must have a \description
checkRd: (5) hlogis.Rd:0-29: Must have a \description
checkRd: (5) hnorm.Rd:0-31: Must have a \description
checkRd: (5) hstudent.Rd:0-32: Must have a \description
checkRd: (5) hweibull.Rd:0-31: Must have a \description
checkRd: (5) ident.Rd:0-31: Must have a \description
checkRd: (5) pp.Rd:0-29: Must have a \description
checkRd: (5) tccov.Rd:0-33: Must have a \description
checkRd: (5) tpast.Rd:0-27: Must have a \description
checkRd: (5) ttime.Rd:0-31: Must have a \description
checkRd: (5) tvcov.Rd:0-32: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'event.Rd':
  ‘[event]{hboxcox}’ ‘[event]{hburr}’ ‘[event]{hgextval}’
  ‘[event]{hggamma}’ ‘[event]{hglogis}’ ‘[event]{hgweibull}’
  ‘[event]{hhjorth}’ ‘[event]{hinvgauss}’ ‘[event]{hlaplace}’
  ‘[event]{hpareto}’ ‘[event]{hskewlaplace}’ ‘[event]{read.list}’
  ‘[event]{read.surv}’

Missing link or links in documentation object 'hcauchy.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hexp.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hgamma.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hlnorm.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hlogis.Rd':
  ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hhjorth’ ‘hinvgauss’
  ‘hlaplace’ ‘hglogis’ ‘hgweibull’

Missing link or links in documentation object 'hnorm.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hstudent.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'hweibull.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'km.Rd':
  ‘[event]{plot.survivor}’

Missing link or links in documentation object 'plot.intensity.Rd':
  ‘[event]{plot.survivor}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘autointensity’ ‘baseline’ ‘baseline.survivalkit’
  ‘deviance.intensity’ ‘deviance.kalsurv’ ‘deviance.pbirth’
  ‘fitted.kalsurv’ ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hglogis’
  ‘hgweibull’ ‘hhjorth’ ‘hinvgauss’ ‘hlaplace’ ‘hpareto’ ‘hskewlaplace’
  ‘plot.intensity.default’ ‘plot.surv’ ‘print.intensity’
  ‘print.kalsurv’ ‘print.km’ ‘print.llrf’ ‘print.pbirth’
  ‘print.survivalkit’ ‘residuals.kalsurv’ ‘residuals.survivalkit’
  ‘survival’ ‘survival.survivalkit’ ‘vdm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autointensity':
autointensity
  Code: function(times, window = NULL, maxlag = max(times), ylab =
                 "Conditional probability", xlab = "Lag", main =
                 "Autointensity function", xlim = c(0, max(times)),
                 ylim = c(0, if (plotse) max(se1) else max(z$density)),
                 lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
  Docs: function(times, window = NULL, maxlag = total/10, ylab =
                 "Conditional probability", xlab = "Lag", main =
                 "Autointensity function", xlim = c(0, max(times)),
                 ylim = c(0, if (plotse) max(se1) else max(z$density)),
                 lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
  Mismatches in argument default values:
    Name: 'maxlag' Code: max(times) Docs: total/10

Codoc mismatches from documentation object 'coxre':
coxre
  Code: function(response, censor, nest = NULL, cov = NULL, stratified
                 = FALSE, cumul = FALSE, estimate = 1, iter = 10,
                 print.level = 0, ndigit = 10, gradtol = 1e-05, steptol
                 = 1e-05, iterlim = 100, fscale = 1, typsize =
                 abs(estimate), stepmax = estimate)
  Docs: function(response, censor, nest = NULL, cov = NULL, stratified
                 = FALSE, cumul = FALSE, estimate = 1, iter = 10,
                 print.level = 0, ndigit = 10, gradtol = 1e-05, steptol
                 = 1e-05, iterlim = 100, fscale = 1, typsiz =
                 abs(estimate), stepmax = estimate)
  Argument names in code not in docs:
    typsize
  Argument names in docs not in code:
    typsiz
  Mismatches in argument names:
    Position: 15 Code: typsize Docs: typsiz

Codoc mismatches from documentation object 'ehr':
ehr
  Code: function(point, lambda = NULL, linear = NULL, plambda = NULL,
                 delta = 1, envir = parent.frame(), print.level = 0,
                 typsize = rep(1, length(plambda)), ndigit = 10,
                 gradtol = 1e-05, iterlim = 100, fscale = 1, stepmax =
                 max(10 * sqrt(plambda %*% plambda), 10), steptol =
                 4e-04)
  Docs: function(point, lambda = NULL, linear = NULL, plambda = NULL,
                 delta = 1, envir = parent.frame(), print.level = 0,
                 typsiz = rep(1, length(plambda)), ndigit = 10, gradtol
                 = 1e-05, iterlim = 100, fscale = 1, stepmax = max(10 *
                 sqrt(plambda %*% plambda), 10), steptol = 4e-04)
  Argument names in code not in docs:
    typsize
  Argument names in docs not in code:
    typsiz
  Mismatches in argument names:
    Position: 8 Code: typsize Docs: typsiz

Codoc mismatches from documentation object 'kalsurv':
kalsurv
  Code: function(response = NULL, intensity = "exponential",
                 distribution = "Pareto", depend = "independence",
                 update = "Markov", mu = NULL, shape = NULL, renewal =
                 TRUE, density = FALSE, censor = NULL, delta = NULL,
                 ccov = NULL, tvcov = NULL, preg = NULL, ptvc = NULL,
                 pbirth = NULL, pintercept = NULL, pshape = NULL,
                 pinitial = 1, pdepend = NULL, pfamily = NULL, envir =
                 parent.frame(), print.level = 0, ndigit = 10, gradtol
                 = 1e-05, steptol = 1e-05, iterlim = 100, fscale = 1,
                 typsize = abs(p), stepmax = 10 * sqrt(p %*% p))
  Docs: function(response, intensity = "exponential", distribution =
                 "Pareto", depend = "independence", update = "Markov",
                 mu = NULL, shape = NULL, renewal = TRUE, density =
                 FALSE, censor = NULL, delta = NULL, ccov = NULL, tvcov
                 = NULL, preg = 1, ptvc = NULL, pbirth = NULL,
                 pintercept = NULL, pshape = NULL, pinitial = 1,
                 pdepend = NULL, pfamily = NULL, envir =
                 parent.frame(), print.level = 0, ndigit = 10, gradtol
                 = 1e-05, steptol = 1e-05, iterlim = 100, fscale = 1,
                 typsiz = abs(p), stepmax = 10 * sqrt(p %*% p))
  Argument names in code not in docs:
    typsize
  Argument names in docs not in code:
    typsiz
  Mismatches in argument names:
    Position: 29 Code: typsize Docs: typsiz
  Mismatches in argument default values:
    Name: 'response' Code: NULL Docs: 
    Name: 'preg' Code: NULL Docs: 1

Codoc mismatches from documentation object 'km':
plot.intensity.km
  Code: function(z, add = FALSE, xlab = "Time", ylab = "Hazard", type =
                 "l", lty = NULL, ...)
  Docs: function(z, add = FALSE, xlab = "Time", ylab = "Intensity",
                 type = "l", lty = NULL, ...)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Hazard" Docs: "Intensity"

Codoc mismatches from documentation object 'pbirth':
pbirth
  Code: function(frequencies, p, intensity = "negative binomial", type
                 = "spectral decomposition", print.level = 0, ndigit =
                 10, gradtol = 1e-05, steptol = 1e-05, fscale = 1,
                 iterlim = 100, typsize = abs(p), stepmax = 10 * sqrt(p
                 %*% p))
  Docs: function(frequencies, p, intensity = "negative binomial", type
                 = "spectral decomposition", print.level = 0, ndigit =
                 10, gradtol = 1e-05, steptol = 1e-05, fscale = 1,
                 iterlim = 100, typsiz = abs(p), stepmax = 10 * sqrt(p
                 %*% p))
  Argument names in code not in docs:
    typsize
  Argument names in docs not in code:
    typsiz
  Mismatches in argument names:
    Position: 11 Code: typsize Docs: typsiz

Codoc mismatches from documentation object 'plot.intensity':
plot.intensity.default
  Code: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
                 ylim = c(0, 1), ylab = "p", xlab = "Time", main =
                 "Empirical Hazard Function(s)")
  Docs: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
                 ylim = c(0, 1), ylab = "p", xlab = "Time", main =
                 "Empirical Intensity Function(s)")
  Mismatches in argument default values:
    Name: 'main' Code: "Empirical Hazard Function(s)" Docs: "Empirical Intensity Function(s)"

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'autointensity'
  ‘ylab’ ‘xlab’ ‘main’ ‘xlim’ ‘ylim’ ‘lty’ ‘...’
Documented arguments not in \usage in documentation object 'autointensity':
  ‘others’
Objects in \usage without \alias in documentation object 'autointensity':
  ‘autointensity’

Undocumented arguments in documentation object 'coxre'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
  ‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'coxre':
  ‘others’

Undocumented arguments in documentation object 'cprocess'
  ‘lty’ ‘xlim’ ‘ylim’ ‘xlab’ ‘ylab’ ‘...’
Documented arguments not in \usage in documentation object 'cprocess':
  ‘others’

Undocumented arguments in documentation object 'ehr'
  ‘print.level’ ‘typsiz’ ‘ndigit’ ‘gradtol’ ‘iterlim’ ‘fscale’
  ‘stepmax’ ‘steptol’
Documented arguments not in \usage in documentation object 'ehr':
  ‘others’

Undocumented arguments in documentation object 'kalsurv'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
  ‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'kalsurv':
  ‘others’

Undocumented arguments in documentation object 'km'
  ‘add’ ‘xlim’ ‘ylim’ ‘main’ ‘xlab’ ‘ylab’ ‘lty’ ‘...’ ‘type’

Undocumented arguments in documentation object 'pbirth'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’
  ‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'pbirth':
  ‘others’

Undocumented arguments in documentation object 'plot.intensity'
  ‘z’ ‘...’ ‘mix’ ‘ylim’ ‘ylab’ ‘xlab’ ‘main’
Objects in \usage without \alias in documentation object 'plot.intensity':
  ‘plot.intensity.default’

Undocumented arguments in documentation object 'pp'
  ‘censor’
Documented arguments not in \usage in documentation object 'pp':
  ‘cens’

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 'km':
  ‘plot.km’ ‘plot.intensity.km’ ‘plot.dist.km’

S3 methods shown with full name in documentation object 'plot.intensity':
  ‘plot.intensity’ ‘plot.intensity.default’

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 ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘event-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pbirth
> ### Title: Fit Overdispersed Count Data as a Birth Process
> ### Aliases: pbirth
> ### Keywords: models
> 
> ### ** Examples
> 
> y <- rnbinom(100,2,0.6)
> fr <- tabulate(y)
> pbirth(fr, p=log(-log(0.7)), intensity="Poisson", type="series")
Error in log(prob1(p)) : non-numeric argument to mathematical function
Calls: pbirth -> nlm -> <Anonymous> -> f
Execution halted
* DONE
Status: 1 ERROR, 7 WARNINGs, 2 NOTEs
checking examples ... ERROR
Running examples in ‘event-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pbirth
> ### Title: Fit Overdispersed Count Data as a Birth Process
> ### Aliases: pbirth
> ### Keywords: models
> 
> ### ** Examples
> 
> y <- rnbinom(100,2,0.6)
> fr <- tabulate(y)
> pbirth(fr, p=log(-log(0.7)), intensity="Poisson", type="series")
Error in log(prob1(p)) : non-numeric argument to mathematical function
Calls: pbirth -> nlm -> <Anonymous> -> f
Execution halted

checking whether package ‘event’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Rank mismatch in argument 'valrho' at (1) (rank-1 and scalar)
See ‘/Users/swihartbj/github/event.Rcheck/00install.out’ for details.

checking S3 generic/method consistency ... WARNING
baseline:
  function(z, ...)
baseline.survivalkit:
  function(z)

plot.dist:
  function(z, ...)
plot.dist.km:
  function(z)
... 109 lines ...
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  baseline.survivalkit deviance.intensity deviance.kalsurv
  deviance.pbirth fitted.kalsurv plot.dist plot.dist.km plot.dist.km
  plot.intensity plot.intensity.default plot.intensity.default
  plot.intensity.km plot.intensity.km plot.km plot.surv print.intensity
  print.kalsurv print.km print.llrf print.pbirth print.survivalkit
  residuals.kalsurv residuals.survivalkit survival.survivalkit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking Rd files ... WARNING
checkRd: (5) bp.Rd:0-32: Must have a \description
checkRd: (5) hcauchy.Rd:0-31: Must have a \description
checkRd: (5) hexp.Rd:0-30: Must have a \description
checkRd: (5) hgamma.Rd:0-32: Must have a \description
checkRd: (5) hlnorm.Rd:0-31: Must have a \description
checkRd: (5) hlogis.Rd:0-29: Must have a \description
checkRd: (5) hnorm.Rd:0-31: Must have a \description
checkRd: (5) hstudent.Rd:0-32: Must have a \description
checkRd: (5) hweibull.Rd:0-31: Must have a \description
checkRd: (5) ident.Rd:0-31: Must have a \description
checkRd: (5) pp.Rd:0-29: Must have a \description
checkRd: (5) tccov.Rd:0-33: Must have a \description
checkRd: (5) tpast.Rd:0-27: Must have a \description
checkRd: (5) ttime.Rd:0-31: Must have a \description
checkRd: (5) tvcov.Rd:0-32: Must have a \description

checking Rd cross-references ... WARNING
Missing link or links in documentation object 'event.Rd':
  ‘[event]{hboxcox}’ ‘[event]{hburr}’ ‘[event]{hgextval}’
  ‘[event]{hggamma}’ ‘[event]{hglogis}’ ‘[event]{hgweibull}’
  ‘[event]{hhjorth}’ ‘[event]{hinvgauss}’ ‘[event]{hlaplace}’
  ‘[event]{hpareto}’ ‘[event]{hskewlaplace}’ ‘[event]{read.list}’
  ‘[event]{read.surv}’

Missing link or links in documentation object 'hcauchy.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
... 34 lines ...
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
  ‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
  ‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’

Missing link or links in documentation object 'km.Rd':
  ‘[event]{plot.survivor}’

Missing link or links in documentation object 'plot.intensity.Rd':
  ‘[event]{plot.survivor}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘autointensity’ ‘baseline’ ‘baseline.survivalkit’
  ‘deviance.intensity’ ‘deviance.kalsurv’ ‘deviance.pbirth’
  ‘fitted.kalsurv’ ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hglogis’
  ‘hgweibull’ ‘hhjorth’ ‘hinvgauss’ ‘hlaplace’ ‘hpareto’ ‘hskewlaplace’
  ‘plot.intensity.default’ ‘plot.surv’ ‘print.intensity’
  ‘print.kalsurv’ ‘print.km’ ‘print.llrf’ ‘print.pbirth’
  ‘print.survivalkit’ ‘residuals.kalsurv’ ‘residuals.survivalkit’
  ‘survival’ ‘survival.survivalkit’ ‘vdm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autointensity':
autointensity
  Code: function(times, window = NULL, maxlag = max(times), ylab =
                 "Conditional probability", xlab = "Lag", main =
                 "Autointensity function", xlim = c(0, max(times)),
                 ylim = c(0, if (plotse) max(se1) else max(z$density)),
                 lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
  Docs: function(times, window = NULL, maxlag = total/10, ylab =
                 "Conditional probability", xlab = "Lag", main =
... 105 lines ...

Codoc mismatches from documentation object 'plot.intensity':
plot.intensity.default
  Code: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
                 ylim = c(0, 1), ylab = "p", xlab = "Time", main =
                 "Empirical Hazard Function(s)")
  Docs: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
                 ylim = c(0, 1), ylab = "p", xlab = "Time", main =
                 "Empirical Intensity Function(s)")
  Mismatches in argument default values:
    Name: 'main' Code: "Empirical Hazard Function(s)" Docs: "Empirical Intensity Function(s)"

checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'autointensity'
  ‘ylab’ ‘xlab’ ‘main’ ‘xlim’ ‘ylim’ ‘lty’ ‘...’
Documented arguments not in \usage in documentation object 'autointensity':
  ‘others’
Objects in \usage without \alias in documentation object 'autointensity':
  ‘autointensity’

Undocumented arguments in documentation object 'coxre'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
... 45 lines ...
Extensions’ manual.
S3 methods shown with full name in documentation object 'km':
  ‘plot.km’ ‘plot.intensity.km’ ‘plot.dist.km’

S3 methods shown with full name in documentation object 'plot.intensity':
  ‘plot.intensity’ ‘plot.intensity.default’

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 foreign function calls ... NOTE
Calls with DUP:
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
... 72 lines ...
       iplus1 = as.integer(iplus1), iplus2 = as.integer(iplus2), 
       ipedig = as.integer(pedigree), nrr2 = as.integer(nrr2), nccov = as.integer(nccov), 
       ndcov = as.integer(ndcov), nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), km = double(nrr * 
           nstrata * 4), resid = double(nrr * nstrata * 3), ut = as.integer(nrr * 
           nstrata), DUP = FALSE, PACKAGE = "event")
DUP is no longer supported and will be ignored.

checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

autointensity: no visible global function definition for ‘hist’
autointensity: no visible global function definition for ‘lines’
coxre : like: no visible global function definition for ‘glm’
coxre : like: no visible binding for global variable ‘poisson’
coxre : likel: no visible global function definition for ‘glm’
coxre : likel: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘glm’
... 46 lines ...
  dcauchy dgamma dlnorm dlogis dnorm glm gray hist lines model.frame
  na.fail nlm npl1 par pbeta pcauchy pgamma plnorm plogis plot pnorm
  poisson pweibull qnorm terms text
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "hist", "lines", "par", "plot", "text")
  importFrom("stats", "dcauchy", "dgamma", "dlnorm", "dlogis", "dnorm",
             "glm", "model.frame", "na.fail", "nlm", "pbeta", "pcauchy",
             "pgamma", "plnorm", "plogis", "pnorm", "poisson",
             "pweibull", "qnorm", "terms")
to your NAMESPACE file.

See
  ‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.

R CMD check results
1 error  | 7 warnings | 2 notes

R CMD check succeeded

[swihart]

Oh man, this was instructional for S3 consistency:

https://github.com/ropensci/neotoma/issues/117

In km.r, I added in x as first argument because I can't rewrite the generic. I'm nervous as to what it might do.

### function to plot survivor curves
###
plot.surv <- function(x, times=NULL, survivor, group=1, cdf=FALSE, add=FALSE,
    xlim=NULL, ylim=c(0,1), main=NULL, xlab="Time", ylab=NULL, lty=NULL,
    ...){
if(missing(times)||missing(survivor))
    stop("times and survivor curve must be supplied")

Ah, I undid it. Work on the other ones first. These plot extensions are tricky!

[swihart]

Okay, I think I did it. We're 1e|1w|0n now.

1 error  | 1 warning  | 0 notes

[swihart]

Cool. So had to do some Terminal

R CMD build event and R CMD check event_1.1.0_tar.gz

and then emacs the event.Rcheck/00installout to see the .c and .f stuff.

Basically removed kk from the two .c files and then made

valrho(MXSTRA) into valrho(MXSTRA) at line 4655 of survkit.f

And ---

R CMD check results
1 error  | 0 warnings | 0 notes

R CMD check succeeded

[swihart]

Fix examples.

R CMD check results
0 errors | 0 warnings | 0 notes

R CMD check succeeded

You're welcome.