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armlite log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck'
* using R version 3.2.2 Patched (2015-11-05 r69602)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'armlite/DESCRIPTION' ... OK
* this is package 'armlite' version '0.00-15'
* checking CRAN incoming feasibility ...Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/coefplot.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/display.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/se.coef.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/sigma.hat.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/sim.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/standardize.Rd: docType 'genericFunction' is unrecognized
Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/traceplot.Rd: docType 'genericFunction' is unrecognized
 NOTE
Maintainer: 'Yu-Sung Su '
New submission

Version contains leading zeroes (0.00-15)

Uses the non-portable package: 'R2WinBUGS'
Found the following (possibly) invalid URLs:
  URL: http://elsa.berkeley.edu/~imbens/matlab/lalonde_exper_04feb2.m (moved to http://eml.berkeley.edu//~imbens/matlab/lalonde_exper_04feb2.m)
    From: man/lalonde.Rd
    Status: 404
    Message: Not Found

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'armlite' can be installed ... WARNING
Found the following significant warnings:
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/coefplot.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/display.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/se.coef.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/sigma.hat.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/sim.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/standardize.Rd: docType 'genericFunction' is unrecognized
  Warning: R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00_pkg_src/armlite/man/traceplot.Rd: docType 'genericFunction' is unrecognized
See 'R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'R2WinBUGS'
  Please remove these calls from your code.
'library' or 'require' call to 'foreign' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'MASS' 'R2WinBUGS' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  model.matrix.bayes
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call to a base package:
  .Fortran("dqrls", ..., PACKAGE = "base")
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... WARNING
Found .Internal calls in the following functions:
  'model.matrix.bayes' 'model.matrix.bayes.h'
with calls to .Internal functions
  'model.matrix'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.

In addition to the above warning(s), found the following notes:

File 'armlite/R/load.first.R':
  .onAttach calls:
    cat(paste("\narmlite (Version ", ver, ", built: ", builddate,     ")\n", sep = ""))
    cat("Working directory is", getwd(), "\n")
    require(foreign)
    require(MASS)
    require(R2WinBUGS)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

.onAttach: warning in packageDescription("armlite", lib = mylib):
  partial argument match of 'lib' to 'lib.loc'
mcplot: warning in axis(2, at = 0, label = "", las = 1, line = 0, tick
  = FALSE, xaxs = "i", yaxs = "i"): partial argument match of 'label'
  to 'labels'
multicomp.plot: warning in axis(2, at = 0, label = "", las = 1, line =
  0, tick = FALSE, xaxs = "i", yaxs = "i"): partial argument match of
  'label' to 'labels'
triangleplot: warning in rect(xleft = 0.5, ybottom =
  z.breaks[length(z.breaks)], xright = 1, y =
  z.breaks[length(z.breaks)], col = z.colors[length(z.colors)]):
  partial argument match of 'y' to 'ytop'
sim,glm : .local: no visible global function definition for 'mvrnorm'
sim,lm : .local: no visible global function definition for 'mvrnorm'
traceplot,mcmc.list : .local: no visible global function definition for
  'nvar'
traceplot,mcmc.list : .local: no visible global function definition for
  'varnames'
traceplot,mcmc.list : .local: no visible global function definition for
  'nchain'
* checking Rd files ... WARNING
prepare_Rd: coefplot.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: display.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: se.coef.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: sigma.hat.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: sim.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: standardize.Rd: docType 'genericFunction' is unrecognized
prepare_Rd: traceplot.Rd: docType 'genericFunction' is unrecognized
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'residual.plot.Rd':
  \usage lines wider than 90 characters:
     residual.plot(Expected, Residuals, sigma, main = deparse(substitute(Expected)), col.pts = "blue", col.ctr = "red", col.sgm = "black", c ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'Matching'
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'model.matrix.bayes':
  'model.matrix.bayes'

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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'armlite-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: balance
> ### Title: Functions to compute the balance statistics
> ### Aliases: balance-class balance print.balance plot.balance
> ### Keywords: methods manip hplot dplot
> 
> ### ** Examples
> 
> # matching first
> old.par <- par(no.readonly = TRUE)
> data(lalonde)
> attach(lalonde)
> fit <- glm(treat ~ re74 + re75 + age + factor(educ) + 
+             black + hisp + married + nodegr + u74 + u75, 
+             family=binomial(link="logit"))
> pscores <- predict(fit, type="link")
> matches <- matching(z=lalonde$treat, score=pscores)
> matched <- lalonde[matches$matched,]
> 
> # balance check
> b.stats <- balance(lalonde, matched, fit)
Error in .Internal(model.matrix(t, data)) : 
  there is no .Internal function 'model.matrix'
Calls: balance -> model.matrix.bayes
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 7 NOTEs
See
  'R:/run/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/armlite.Rcheck/00check.log'
for details.

Run time: 50.89 seconds.