Package: genefilter

Version: 1.14.1

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check genefilter_1.14.1.tar.gz

RetCode: 0

Time: 183.1 seconds

Status: OK

CheckDir: genefilter.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.0-bioc/meat/genefilter.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.14.1'
* checking package dependencies ... OK
* 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 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 whether the name space 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 ... OK
* checking data for non-ASCII characters ... 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 ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating genefilter-manual.tex ... OK
* checking genefilter-manual.tex ... OK

* Installing *source* package 'genefilter' ...
** libs
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nd.c -o nd.o
nd.c: In function `gf_dist_binary':
nd.c:219: warning: unused variable `w1'
nd.c:219: warning: unused variable `w2'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function `pAUC_c':
pAUC.c:75: warning: operation on `ta' may be undefined
pAUC.c:78: warning: operation on `ta' may be undefined
pAUC.c:81: warning: operation on `ta' may be undefined
pAUC.c: In function `pAUC':
pAUC.c:141: warning: suggest parentheses around comparison in operand of |
pAUC.c:123: warning: unused variable `i'
pAUC.c: In function `pAUC_c':
pAUC.c:22: warning: `xsum' might be used uninitialized in this function
pAUC.c:22: warning: `ysum' might be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c: In function `ROCpAUC_c':
rowPAUCs.c:95: warning: operation on `ta' may be undefined
rowPAUCs.c:98: warning: operation on `ta' may be undefined
rowPAUCs.c:101: warning: operation on `ta' may be undefined
rowPAUCs.c:23: warning: `xsum' might be used uninitialized in this function
rowPAUCs.c:23: warning: `ysum' might be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowttests.c -o rowttests.o
g77   -fpic  -g -O2 -Wall -c ttest.f -o ttest.o
g++ -shared -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o  -lg2c -lm -lgcc_s -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
**  moving datasets to lazyload DB
** inst
** save image
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: survival
Loading required package: splines
Creating a new generic function for "plot" in "genefilter"
** 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
  nsFilter                          text    html    latex   example
  pOverA                            text    html    latex   example
  rowFtests                         text    html    latex   example
  rowROC-class                      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)