Package: genefilter

Version: 1.38.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings genefilter_1.38.0.tar.gz

StartedAt: 2012-04-01 01:05:15 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:06:51 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 96.4 seconds

RetCode: 0

Status:  OK

CheckDir: genefilter.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/genefilter.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'genefilter' can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
File 'genefilter/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)
    require("Biobase")

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

eSetFilter : buildGUI: no visible binding for '<<-' assignment to 'END'
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
  to 'END'
eSetFilter : buildGUI: no visible binding for global variable 'END'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/genefilter.Rcheck/00check.log'
for details.

* installing *source* package 'genefilter' ...
** libs
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c nd.c -o nd.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pAUC.c -o pAUC.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowPAUCs.c -o rowPAUCs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2  -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 -lgfortran -lm -lquadmath -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/genefilter.Rcheck/genefilter/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'genefilter'
** help
*** installing help indices
** building package indices
** installing vignettes
   'howtogenefilter.Rnw' 
   'howtogenefinder.Rnw' 
   'independent_filtering_plots.Rnw' 
** testing if installed package can be loaded

* DONE (genefilter)

name	user	system	elapsed
Anova	0.012	0.000	0.013
allNA	0.004	0.000	0.000
coxfilter	0.08	0.00	0.08
cv	0	0	0
dist2	0.004	0.000	0.004
eSetFilter	0	0	0
filter_volcano	0	0	0
filtered_p	0	0	0
filterfun	0.000	0.000	0.001
findLargest	0.764	0.048	0.899
gapFilter	0.004	0.000	0.001
genefilter	0.004	0.000	0.006
genefinder	0.060	0.012	0.070
genescale	0	0	0
half.range.mode	3.880	0.000	3.879
kOverA	0	0	0
kappa_p	0	0	0
maxA	0.004	0.000	0.000
nsFilter	0.464	0.020	0.551
pOverA	0	0	0
rejection_plot	0	0	0
rowFtests	5.672	0.020	5.697
rowROC-class	0.108	0.004	0.141
rowSds	0.004	0.000	0.001
rowpAUCs	1.460	0.008	1.507
shorth	0.000	0.000	0.001
tdata	0.004	0.000	0.008
ttest	0.004	0.000	0.005