Package: maigesPack

Version: 1.20.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.20.0.tar.gz

StartedAt: 2012-04-01 01:58:14 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:03:31 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 317.6 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/maigesPack.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 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.20.0'
* 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 'maigesPack' 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 ... OK
* 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

* installing *source* package 'maigesPack' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c register.c -o register.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'show' when loading 'limma'
** help
*** installing help indices
** building package indices
** installing vignettes
   'maigesPack_tutorial.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'show' when loading 'limma'

* DONE (maigesPack)

name	user	system	elapsed
MI	0.004	0.000	0.003
activeMod	2.396	0.012	2.417
activeModScoreHTML	1.432	0.008	1.450
activeNet	4.444	0.012	4.468
activeNetScoreHTML	4.428	0.004	4.445
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.048	0.000	0.051
bootstrapMI	0.284	0.000	0.282
bootstrapT	0.004	0.000	0.004
boxplot-methods	64.484	1.700	66.219
bracketMethods	0.228	0.000	0.240
calcA	0.164	0.072	0.253
calcW	0.176	0.056	0.241
classifyKNN	0.257	0.000	0.269
classifyKNNsc	0.436	0.008	0.454
classifyLDA	1.120	0.008	1.144
classifyLDAsc	1.928	0.004	1.942
classifySVM	0.572	0.000	0.586
classifySVMsc	0.956	0.000	0.966
coerce-methods	0.140	0.004	0.152
compCorr	0	0	0
createMaigesRaw	0.360	0.004	0.371
deGenes2by2BootT	0.528	0.012	0.551
deGenes2by2Ttest	0.296	0.000	0.305
deGenes2by2Wilcox	0.264	0.004	0.277
deGenesANOVA	0.356	0.000	0.371
designANOVA	0.132	0.004	0.145
dim-methods	0.072	0.004	0.086
getLabels	0.072	0.004	0.085
hierM	1.860	0.020	1.855
hierMde	0.512	0.004	0.534
image-methods	2.904	0.012	2.926
kmeansM	1.768	0.024	1.791
kmeansMde	0.416	0.000	0.422
loadData	0	0	0
normLoc	2.181	0.004	2.194
normOLIN	0.072	0.000	0.082
normRepLoess	0.076	0.000	0.086
normScaleLimma	78.692	0.920	79.739
normScaleMarray	42.923	0.824	43.774
plot-methods	7.681	0.012	7.710
plotGenePair	0.108	0.008	0.125
print-methods	0.152	0.004	0.164
relNet2TGF	0.152	0.000	0.163
relNetworkB	1.828	0.020	1.854
relNetworkM	0.092	0.008	0.112
robustCorr	0	0	0
selSpots	0.260	0.008	0.280
show-methods	0.152	0.000	0.158
somM	1.912	0.016	1.932
somMde	0.420	0.000	0.431
summarizeReplicates	1.964	0.000	1.975
summary-methods	0.156	0.004	0.170
tableClass	0.808	0.012	0.835
tablesDE	2.836	0.028	2.933