Package: DNAcopy

Version: 1.11.1

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check DNAcopy_1.11.1.tar.gz

RetCode: 0

Time: 25.5 seconds

Status: OK

CheckDir: DNAcopy.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/DNAcopy.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.11.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DNAcopy' 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 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 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 ... 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DNAcopy':
  plot.DNAcopy

S3 methods shown with full name in documentation object 'subset.CNA':
  subset.CNA

S3 methods shown with full name in documentation object 'subset.DNAcopy':
  subset.DNAcopy

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating DNAcopy-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating DNAcopy-manual.tex ... OK
* checking DNAcopy-manual.tex ... OK

* Installing *source* package 'DNAcopy' ...
** libs
gfortran   -fpic  -g -O2 -Wall -c changepoints.f -o changepoints.o
changepoints.f: In function 'tmax1':
changepoints.f:175: warning: 'wtmxj' may be used uninitialized in this function
changepoints.f:175: warning: 'wtmxi' may be used uninitialized in this function
changepoints.f:175: warning: 'sxmxi' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran   -fpic  -g -O2 -Wall -c getbdry.f -o getbdry.o
getbdry.f: In function 'getbdry':
getbdry.f:1: warning: unused variable 'i'
getbdry.f:1: warning: unused variable 'k'
gfortran   -fpic  -g -O2 -Wall -c hybcpt.f -o hybcpt.o
gfortran   -fpic  -g -O2 -Wall -c prune.f -o prune.o
prune.f: In function 'combn':
prune.f:100: warning: unused variable 'n'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rshared.c -o rshared.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DNAcopy.so changepoints.o flchoose.o fphyper.o fpnorm.o getbdry.o hybcpt.o prune.o rshared.o  -lgfortran -lm -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** help
Note: unmatched right brace in 'segment' on or after line 60
 >>> Building/Updating help pages for package 'DNAcopy'
     Formats: text html latex example 
  CNA                               text    html    latex   example
  DNAcopy-internal                  text    html    latex
  DNAcopy                           text    html    latex
  coriell                           text    html    latex
  cytoBand                          text    html    latex
  getbdry                           text    html    latex
  plot.DNAcopy                      text    html    latex   example
  segment                           text    html    latex   example
  smooth.CNA                        text    html    latex   example
  subset.CNA                        text    html    latex   example
  subset.DNAcopy                    text    html    latex
** building package indices ...
* DONE (DNAcopy)