CHECK report for pairseqsim on gopher5

* checking for working latex ... OK * using log directory '/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 /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/lib64 -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)

Package 137/205	OS	Arch	BUILD	CHECK	BUILD BIN
pairseqsim 1.7.0 Witold Wolski	Linux (SUSE 9.2)	x86_64	OK	[ WARNINGS ]
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	OK
	Linux (SUSE 10.0)	x86_64	OK	WARNINGS
	Windows Server 2003	x86_64	OK	WARNINGS	OK
	Windows XP	i686	OK	WARNINGS	skipped
	Mac OS X (10.4.6)	i686	OK	WARNINGS

pairseqsim

1.7.0

Command output