Package: pairseqsim

Version: 1.7.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check pairseqsim_1.7.0.tar.gz

RetCode: 0

Time: 90.8 seconds

Status: WARNINGS

CheckDir: pairseqsim.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/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 for sufficient/correct file permissions ... 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
  /extra/loc/biocbuild/1.9d/Rpacks/pairseqsim.Rcheck/00check.log
for details

* Installing *source* package 'pairseqsim' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c align.c -o align.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c basic.c -o basic.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c callalign.c -o callalign.o
gcc -shared -L/usr/local/lib -o pairseqsim.so align.o basic.o callalign.o   
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'pairseqsim'
     Formats: text html latex example 
  AAAlignment-class                 text    html    latex   example
  AAAlphabet-class                  text    html    latex   example
  AASequence-class                  text    html    latex   example
  AASequence                        text    html    latex   example
  AASequenceList-class              text    html    latex   example
  EPAM110                           text    html    latex   example
  Submatrix-class                   text    html    latex
  listdist-methods                  text    html    latex
  readFasta-methods                 text    html    latex   example
  salign-methods                    text    html    latex   example
  sequlist                          text    html    latex   example
  testalign-methods                 text    html    latex
** building package indices ...
* DONE (pairseqsim)