Package: pairseqsim

Version: 1.7.0

Command: E:\hpages\1.9d\R\bin\R.exe CMD check pairseqsim_1.7.0.tar.gz

RetCode: 0

Time: 79.1 seconds

Status: WARNINGS

CheckDir: pairseqsim.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory 'E:/hpages/1.9d/Rpacks/pairseqsim.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'pairseqsim/DESCRIPTION' ... OK
* this is package 'pairseqsim' version '1.7.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  methods
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'pairseqsim' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... WARNING
Creating a new generic function for 'levels' in 'pairseqsim'
Error in setMethod("frequency", signature(x = "AASequence"), function(x,  : 
	no existing definition for function 'frequency'
Error: unable to load R code in package 'pairseqsim'
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating pairseqsim-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating pairseqsim-manual.tex ... OK
* checking pairseqsim-manual.tex ... OK

WARNING: There were 2 warnings, see
  E:/hpages/1.9d/Rpacks/pairseqsim.Rcheck/00check.log
for details

installing R.css in E:/hpages/1.9d/Rpacks/pairseqsim.Rcheck


---------- Making package pairseqsim ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making align.d from align.c
making basic.d from basic.c
making callalign.d from callalign.c
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c align.c -o align.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c basic.c -o basic.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c callalign.c -o callalign.o
windres --include-dir e:/hpages/1.9d/R/include  -i pairseqsim_res.rc -o pairseqsim_res.o
gcc  -shared -s  -o pairseqsim.dll pairseqsim.def align.o basic.o callalign.o pairseqsim_res.o  -Le:/hpages/1.9d/R/bin   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'pairseqsim'
     Formats: text html latex example chm 
  AAAlignment-class                 text    html    latex   example chm
  AAAlphabet-class                  text    html    latex   example chm
  AASequence-class                  text    html    latex   example chm
  AASequence                        text    html    latex   example chm
  AASequenceList-class              text    html    latex   example chm
  EPAM110                           text    html    latex   example chm
  Submatrix-class                   text    html    latex           chm
  listdist-methods                  text    html    latex           chm
  readFasta-methods                 text    html    latex   example chm
  salign-methods                    text    html    latex   example chm
  sequlist                          text    html    latex   example chm
  testalign-methods                 text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\hpages\1.9d\Rpacks\pairseqsim.Rcheck\00_pkg_src\pairseqsim\chm\pairseqsim.chm


Compile time: 0 minutes, 0 seconds
13	Topics
129	Local links
11	Internet links
1	Graphic


Created e:\hpages\1.9d\Rpacks\pairseqsim.Rcheck\00_pkg_src\pairseqsim\chm\pairseqsim.chm, 28,421 bytes
Compression decreased file by 37,371 bytes.
  adding MD5 sums

* DONE (pairseqsim)