BioC 2.12: CHECK report for genefilter on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.41.1’
* 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 ... 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
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
Examples with CPU or elapsed time > 5s
           user system elapsed
rowFtests 8.725   0.04   8.772
* 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/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/00check.log’
for details.

* installing *source* package ‘genefilter’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-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/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c nd.c -o nd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pAUC.c -o pAUC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowPAUCs.c -o rowPAUCs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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/lib64 -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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	0.028	0.000	0.028
allNA	0.008	0.000	0.011
coxfilter	0.100	0.004	0.105
cv	0.020	0.000	0.015
dist2	0.020	0.000	0.018
eSetFilter	0.008	0.000	0.007
filter_volcano	0.008	0.000	0.007
filtered_p	0.008	0.000	0.007
filterfun	0.012	0.000	0.012
findLargest	0.844	0.032	0.879
gapFilter	0.032	0.000	0.034
genefilter	0.032	0.000	0.029
genefinder	0.428	0.016	0.443
genescale	0.016	0.000	0.016
half.range.mode	4.472	0.012	4.490
kOverA	0.016	0.000	0.015
kappa_p	0.008	0.000	0.008
maxA	0.012	0.000	0.015
nsFilter	0.572	0.016	0.590
pOverA	0.020	0.000	0.021
rejection_plot	0.012	0.004	0.014
rowFtests	8.725	0.040	8.772
rowROC-class	0.188	0.012	0.201
rowSds	0.028	0.000	0.027
rowpAUCs	2.032	0.008	2.045
shorth	0.012	0.004	0.016
tdata	0.004	0.000	0.004
ttest	0.008	0.004	0.013

Summary

Command output