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dpmixsim log file (check_x86_64_linux)

Mon Apr 16 13:14:21 2012: Checking package dpmixsim (SVN revision 142) ...
* using log directory ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/dpmixsim.Rcheck’
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘dpmixsim/DESCRIPTION’ ... OK
* this is package ‘dpmixsim’ version ‘0.0-5’
* checking CRAN incoming feasibility ... WARNING
Insufficient package version (submitted: 0.0.5, existing: 0.0.7)
* 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 whether package ‘dpmixsim’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
postdpmixciz: warning in matrix(res$w, nc = kmax, byr = TRUE): partial
  argument match of 'nc' to 'ncol'
postdpmixciz: warning in matrix(res$w, nc = kmax, byr = TRUE): partial
  argument match of 'byr' to 'byrow'
postdpmixciz: warning in matrix(res$phirec, nc = kmax, byr = TRUE):
  partial argument match of 'nc' to 'ncol'
postdpmixciz: warning in matrix(res$phirec, nc = kmax, byr = TRUE):
  partial argument match of 'byr' to 'byrow'
postdpmixciz: warning in matrix(res$varrec, nc = kmax, byr = TRUE):
  partial argument match of 'nc' to 'ncol'
postdpmixciz: warning in matrix(res$varrec, nc = kmax, byr = TRUE):
  partial argument match of 'byr' to 'byrow'
postdpmixciz: warning in matrix(0, nr = kfreq, nc = ngrid): partial
  argument match of 'nr' to 'nrow'
postdpmixciz: warning in matrix(0, nr = kfreq, nc = ngrid): partial
  argument match of 'nc' to 'ncol'
postdpmixciz: warning in matrix(0, nr = nk, nc = ngrid): partial
  argument match of 'nr' to 'nrow'
postdpmixciz: warning in matrix(0, nr = nk, nc = ngrid): partial
  argument match of 'nc' to 'ncol'
postimgcomps: warning in matrix(1:cl, nc = round(sqrt(cl)), byr =
  TRUE): partial argument match of 'nc' to 'ncol'
postimgcomps: warning in matrix(1:cl, nc = round(sqrt(cl)), byr =
  TRUE): partial argument match of 'byr' to 'byrow'
postkcluster: warning in matrix(1:cl, nr = round(sqrt(cl)), byr =
  TRUE): partial argument match of 'nr' to 'nrow'
postkcluster: warning in matrix(1:cl, nr = round(sqrt(cl)), byr =
  TRUE): partial argument match of 'byr' to 'byrow'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 't1_pn3_rf0_slice_0092.Rd':
  slicedata <- read.sliceimg(fbase = "t1_pn3_rf0", swap = TRUE)

Assignments in \usage in documentation object 't1_pn3_rf0_slice_0092_mask.Rd':
  x <- premask(slicedata, subsamp = TRUE)

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘t1_pn3_rf0_slice_0092.nii.gz’ ‘t1_pn3_rf0_slice_0092_mask.nii.gz’
Please use e.g. ‘inst/extdata’ for non-R data files
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/dpmixsim.Rcheck/dpmixsim/libs/dpmixsim.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘gibbsclustersamplealpha.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘gibbsclustersamplealpha.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [1s/1s] OK
* checking differences from ‘dpmixsim-Ex.Rout’ to ‘dpmixsim-Ex.Rout.save’ ...
2,3c2
< Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'XML'
---
> Creating a new generic function for "image" in "oro.nifti"
5c4
< oro.nifti: Rigorous - NIfTI+ANALYZE+AFNI Input / Output (version = 0.3.1)
---
> oro.nifti: Rigorous - NIfTI Input / Output (version = 0.2.2)
 OK
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
  ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/dpmixsim.Rcheck/00check.log’
for details.

Run time: 47.15 seconds.