R Development Page

alr log file (check_x86_64_linux)

Tue Nov 10 09:53:34 2015: Checking package alr (SVN revision 72) ...
* using log directory ‘/mnt/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/alr.Rcheck’
* using R version 3.2.2 Patched (2015-11-06 r69607)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘alr/DESCRIPTION’ ... OK
* this is package ‘alr’ version ‘0.1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘VJ Carey ’
New submission

The Title field should be in title case, current version then in title case:
‘alternating logistic regression’
‘Alternating Logistic Regression’

The Description field should start with a capital letter.
* 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 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 ‘alr’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘README.splus’
* 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 ... OK
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.alr:
  function(x, digits, quote, prefix)

print:
  function(x, ...)
print.summary.alr:
  function(x, digits, quote, prefix)

summary:
  function(object, ...)
summary.alr:
  function(object)

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

Found the following apparent S3 methods exported but not registered:
  print.alr print.summary.alr summary.alr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘alr/R/zzz.R’:
  .First.lib has wrong argument list ‘a, b’

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
See section ‘Good practice’ in '?.onAttach'.

alr: warning in match.call(expand = FALSE): partial argument match of
  'expand' to 'expand.dots'
class2z: warning in matrix(AAA$ans, nc = ncol(out$z)): partial argument
  match of 'nc' to 'ncol'
alr: no visible binding for global variable ‘response’
* checking Rd files ... WARNING
checkRd: (5) alr.Rd:0-164: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘force.loading’ ‘print.alr’ ‘print.summary.alr’ ‘summary.alr’
Undocumented data sets:
  ‘alr.id’ ‘alr.x’ ‘alr.y’ ‘alr.z’ ‘alr.zid’
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 'alr':
alr
  Code: function(formula = formula(data), id = id, weights = NULL, data
                 = sys.parent(), subset, na.action, contrasts = NULL, z
                 = 0, zmast = 0, zid = 0, zlocs = 0, binit = NULL,
                 ainit, bweight = "full", depmodel = "general",
                 subclust = 0, clnames = NULL, tol = 0.001, maxiter =
                 25, silent = TRUE)
  Docs: function(x, y, id, z = 0, zmast = 0, zid = 0, zlocs = 0, binit,
                 ainit, tol = 0.001, bweight = "full", depmodel =
                 "general", subclust = 0)
  Argument names in code not in docs:
    formula weights data subset na.action contrasts clnames maxiter
    silent
  Argument names in docs not in code:
    x y
  Mismatches in argument names (first 3):
    Position: 1 Code: formula Docs: x
    Position: 2 Code: id Docs: y
    Position: 3 Code: weights Docs: id
  Mismatches in argument default values:
    Name: 'id' Code: id Docs: 
    Name: 'binit' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'class2z':
  ~move the above line to just above the first optional argument

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.
* 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 compiled code ... WARNING
File ‘alr/libs/alr.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘alr.o’, ‘c2z.o’, ‘chanmat.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘alr.o’, ‘chanmat.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘alr.o’, ‘c2z.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘alr.o’, ‘c2z.o’, ‘chanmat.o’, ‘diag_as_vec.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [0s/0s] OK
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2015-11-10-09-29/RF_PKG_CHECK/PKGS/alr.Rcheck/00check.log’
for details.


Run time: 22.93 seconds.