Package: genefilter

Version: 1.41.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefilter_1.41.3.tar.gz

StartedAt: 2013-03-25 02:35:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:37:55 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 152.3 seconds

RetCode: 0

Status:  OK

CheckDir: genefilter.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.41.3'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'genefilter' can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'whbiocvignette.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [27s/28s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
rowFtests       11.289  0.426  11.728
half.range.mode  5.843  0.099   5.948
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'DESeq' 'pasilla'
* 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 were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/00check.log'
for details.

* 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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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-2.12-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
** installing vignettes
   'howtogenefilter.Rnw' 
   'howtogenefinder.Rnw' 
   'independent_filtering.Rnw' 
   'independent_filtering_plots.Rnw' 
** testing if installed package can be loaded
* DONE (genefilter)

name	user	system	elapsed
Anova	0.025	0.006	0.031
allNA	0.007	0.005	0.012
coxfilter	0.085	0.011	0.096
cv	0.007	0.005	0.012
dist2	0.018	0.009	0.028
eSetFilter	0.005	0.006	0.011
filter_volcano	0.003	0.003	0.008
filtered_p	0.003	0.004	0.007
filterfun	0.009	0.007	0.016
findLargest	0.668	0.088	0.761
gapFilter	0.033	0.010	0.043
genefilter	0.019	0.008	0.027
genefinder	0.128	0.048	0.177
genescale	0.010	0.005	0.015
half.range.mode	5.843	0.099	5.948
kOverA	0.012	0.005	0.017
kappa_p	0.009	0.004	0.013
maxA	0.010	0.005	0.016
nsFilter	0.681	0.051	0.743
pOverA	0.019	0.007	0.026
rejection_plot	0.011	0.004	0.015
rowFtests	11.289	0.426	11.728
rowROC-class	0.180	0.033	0.217
rowSds	0.005	0.006	0.011
rowpAUCs	1.852	0.058	1.925
shorth	0.011	0.011	0.023
tdata	0.008	0.008	0.017
ttest	0.016	0.013	0.029