Package: genefilter

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefilter_1.36.0.tar.gz

StartedAt: 2012-03-24 01:12:03 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:14:39 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 155.8 seconds

RetCode: 0

Status:  OK

CheckDir: genefilter.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/genefilter.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.36.0'
* 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 ... NOTE
'library' or 'require' call not declared from: 'ROC'
* 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 sizes of PDF files under '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

* installing *source* package 'genefilter' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c half_range_mode.cpp -o half_range_mode.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c nd.c -o nd.o
nd.c: In function 'gf_dist_binary':
nd.c:242: warning: unused variable 'w2'
nd.c:242: warning: unused variable 'w1'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c pAUC.c -o pAUC.o
pAUC.c: In function 'pAUC_c':
pAUC.c:73: warning: operation on 'ta' may be undefined
pAUC.c:76: warning: operation on 'ta' may be undefined
pAUC.c:79: 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'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c: In function 'ROCpAUC_c':
rowPAUCs.c:97: warning: operation on 'ta' may be undefined
rowPAUCs.c:100: warning: operation on 'ta' may be undefined
rowPAUCs.c:103: warning: operation on 'ta' may be undefined
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowttests.c -o rowttests.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic -c ttest.f -o ttest.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/genefilter.Rcheck/genefilter/libs/i386
** 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 ...
*** tangling vignette sources ...
   'howtogenefilter.Rnw' 
   'howtogenefinder.Rnw' 
   'independent_filtering_plots.Rnw' 
** testing if installed package can be loaded

* DONE (genefilter)

name	user	system	elapsed
Anova	0.023	0.003	0.026
allNA	0.000	0.000	0.001
coxfilter	0.112	0.003	0.116
cv	0.001	0.001	0.001
dist2	0.007	0.002	0.010
eSetFilter	0.000	0.000	0.001
filter_volcano	0	0	0
filtered_p	0.000	0.001	0.000
filterfun	0.001	0.000	0.002
findLargest	0.953	0.055	1.031
gapFilter	0.001	0.000	0.001
genefilter	0.003	0.000	0.004
genefinder	0.112	0.036	0.148
genescale	0.001	0.000	0.001
half.range.mode	7.266	0.143	7.505
kOverA	0.001	0.000	0.001
kappa_p	0.001	0.000	0.000
maxA	0.001	0.000	0.001
nsFilter	0.753	0.040	0.801
pOverA	0.001	0.001	0.000
rejection_plot	0	0	0
rowFtests	10.510	0.526	11.226
rowROC-class	0.363	0.023	0.395
rowSds	0.002	0.001	0.003
rowpAUCs	2.139	0.039	2.226
shorth	0.002	0.000	0.003
tdata	0.001	0.001	0.002
ttest	0.008	0.001	0.008