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Package 177/479HostnameOS / ArchBUILDCHECKBUILD BIN
genefilter 1.35.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefilter
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genefilter
Version: 1.35.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genefilter_1.35.0.tar.gz
StartedAt: 2011-07-07 00:34:40 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 00:35:46 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 65.9 seconds
RetCode: 0
Status:  OK 
CheckDir: genefilter.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genefilter.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.35.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... 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 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

genefilter.Rcheck/00install.out:

* installing *source* package ‘genefilter’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nd.c -o nd.o
nd.c: In function ‘gf_dist_binary’:
nd.c:242:16: warning: unused variable ‘w2’
nd.c:242:12: warning: unused variable ‘w1’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function ‘pAUC_c’:
pAUC.c:73:9: warning: operation on ‘ta’ may be undefined
pAUC.c:76:6: warning: operation on ‘ta’ may be undefined
pAUC.c:79:9: warning: operation on ‘ta’ may be undefined
pAUC.c: In function ‘pAUC’:
pAUC.c:141:5: warning: suggest parentheses around comparison in operand of ‘|’
pAUC.c:123:9: warning: unused variable ‘i’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c: In function ‘ROCpAUC_c’:
rowPAUCs.c:97:9: warning: operation on ‘ta’ may be undefined
rowPAUCs.c:100:6: warning: operation on ‘ta’ may be undefined
rowPAUCs.c:103:9: warning: operation on ‘ta’ may be undefined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2 -Wall -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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘howtogenefilter.Rnw’ 
   ‘howtogenefinder.Rnw’ 
   ‘independent_filtering_plots.Rnw’ 
** testing if installed package can be loaded

* DONE (genefilter)

genefilter.Rcheck/genefilter-Ex.timings:

nameusersystemelapsed
Anova0.0120.0000.011
allNA000
coxfilter0.1720.0040.172
cv0.0000.0000.001
dist20.0080.0000.006
eSetFilter0.0000.0000.001
filter_volcano000
filtered_p000
filterfun0.0040.0000.001
findLargest0.5480.0240.577
gapFilter0.0000.0000.001
genefilter0.0000.0000.002
genefinder0.1800.0240.207
genescale0.0040.0000.001
half.range.mode5.7160.0085.730
kOverA0.0040.0000.000
kappa_p000
maxA000
nsFilter0.4960.0160.513
pOverA000
rejection_plot000
rowFtests5.6040.0605.693
rowROC-class0.2440.0000.243
rowSds0.0000.0000.002
rowpAUCs2.0050.0002.039
shorth0.0000.0000.002
tdata0.0040.0000.002
ttest0.0080.0000.007