Package: DNAcopy

Version: 1.6.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check DNAcopy_1.6.0.tar.gz

RetCode: 0

Time: 137.9 seconds

Status: OK

CheckDir: DNAcopy.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.8d/Rpacks/DNAcopy.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.6.0'
* 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 syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... 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
* 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
g77   -fpic  -g -O2 -Wall -c changepoints.f -o changepoints.o
changepoints.f: In subroutine `tmax1':
changepoints.f:166: warning: `sxmxi' might be used uninitialized in this function
changepoints.f:166: warning: `wtmxi' might be used uninitialized in this function
changepoints.f:166: warning: `wtmxj' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c flchoose.c -o flchoose.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c fphyper.c -o fphyper.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c fpnorm.c -o fpnorm.o
g77   -fpic  -g -O2 -Wall -c getbdry.f -o getbdry.o
getbdry.f: In subroutine `getbdry':
getbdry.f:6: warning: unused variable `k'
getbdry.f:6: warning: unused variable `i'
g77   -fpic  -g -O2 -Wall -c hybcpt.f -o hybcpt.o
g77   -fpic  -g -O2 -Wall -c prune.f -o prune.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c rshared.c -o rshared.o
gcc -shared -L/usr/local/lib -o DNAcopy.so changepoints.o flchoose.o fphyper.o fpnorm.o getbdry.o hybcpt.o prune.o rshared.o  -lg2c -lm -lgcc_s 
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** help
 >>> 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)