Package: genefilter

Version: 1.11.8

Command: /loc/biocbuild/1.9d/R/bin/R CMD check genefilter_1.11.8.tar.gz

RetCode: 0

Time: 147.3 seconds

Status: WARNINGS

CheckDir: genefilter.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/genefilter.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.11.8'
* checking package dependencies ... WARNING
'::' or ':::' imports not declared from:
  tkWidgets
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 'genefilter' 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 ... OK
* checking whether the name space can be loaded with stated dependencies ... 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 ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating genefilter-Ex.R ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: 'hgu95av2LOCUSID' is deprecated.
  Warning: 'hgu95av2LOCUSID' is deprecated.
Deprecated functions may be defunct as soon as of the next release of R.
See ?Deprecated.
* checking package vignettes in 'inst/doc' ... OK
* creating genefilter-manual.tex ... OK
* checking genefilter-manual.tex ... OK

WARNING: There were 2 warnings, see
  /loc/biocbuild/1.9d/Rpacks/genefilter.Rcheck/00check.log
for details

* Installing *source* package 'genefilter' ...
** 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 genedist.c -o genedist.o
genedist.c: In function `mm_dist_binary':
genedist.c:233: warning: unused variable `w1'
genedist.c:233: warning: unused variable `w2'
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp: In function `double half_range_mode(double*, double*, 
   double, int)':
half_range_mode.cpp:55: warning: comparison between signed and unsigned integer 
   expressions
half_range_mode.cpp:68: warning: comparison between signed and unsigned integer 
   expressions
half_range_mode.cpp:76: warning: comparison between signed and unsigned integer 
   expressions
half_range_mode.cpp:14: warning: `double*new_end' might be used uninitialized 
   in this function
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 init.c -o init.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 rowPAUCs.c -o rowPAUCs.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 rowttests.c -o rowttests.o
g77   -fpic  -g -O2 -Wall -c ttest.f -o ttest.o
g++ -shared -L/usr/local/lib64 -o genefilter.so genedist.o half_range_mode.o init.o rowPAUCs.o rowttests.o ttest.o  -lg2c -lm -lgcc_s 
** R
** data
** inst
** save image
Loading required package: Biobase

Loading required package: tools


Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: survival

Loading required package: splines

** help
 >>> Building/Updating help pages for package 'genefilter'
     Formats: text html latex example 
  Anova                             text    html    latex   example
  allNA                             text    html    latex   example
  coxfilter                         text    html    latex   example
  cv                                text    html    latex   example
  eSetFilter                        text    html    latex   example
  filterfun                         text    html    latex   example
  findLargest                       text    html    latex   example
  gapFilter                         text    html    latex   example
  genefilter                        text    html    latex   example
  genefinder                        text    html    latex   example
  genescale                         text    html    latex   example
  half.range.mode                   text    html    latex   example
  kOverA                            text    html    latex   example
  maxA                              text    html    latex   example
  pOverA                            text    html    latex   example
  rowFtests                         text    html    latex   example
  rowSds                            text    html    latex   example
  rowpAUCs                          text    html    latex   example
  shorth                            text    html    latex   example
  tdata                             text    html    latex   example
  ttest                             text    html    latex   example
** building package indices ...
* DONE (genefilter)