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Package 207/554HostnameOS / ArchBUILDCHECKBUILD BIN
genefilter 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/genefilter
Last Changed Rev: 64678 / Revision: 64719
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
puck5 Linux (Ubuntu 12.04) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

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

Command output

* 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.

genefilter.Rcheck/00install.out:

* 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)

genefilter.Rcheck/genefilter-Ex.timings:

nameusersystemelapsed
Anova0.0120.0000.013
allNA0.0040.0000.000
coxfilter0.080.000.08
cv000
dist20.0040.0000.004
eSetFilter000
filter_volcano000
filtered_p000
filterfun0.0000.0000.001
findLargest0.7640.0480.899
gapFilter0.0040.0000.001
genefilter0.0040.0000.006
genefinder0.0600.0120.070
genescale000
half.range.mode3.8800.0003.879
kOverA000
kappa_p000
maxA0.0040.0000.000
nsFilter0.4640.0200.551
pOverA000
rejection_plot000
rowFtests5.6720.0205.697
rowROC-class0.1080.0040.141
rowSds0.0040.0000.001
rowpAUCs1.4600.0081.507
shorth0.0000.0000.001
tdata0.0040.0000.008
ttest0.0040.0000.005