Package: maigesPack

Version: 1.12.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.12.0.tar.gz

StartedAt: 2010-10-04 18:28:13 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:34:42 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 389.4 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/maigesPack.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maigesPack' can be installed ... 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 ... 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'maigesPack' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: limma
Loading required package: marray
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.004	0.000	0.004
activeMod	3.500	0.012	3.830
activeModScoreHTML	1.756	0.008	1.762
activeNet	5.140	0.008	5.149
activeNetScoreHTML	5.141	0.012	5.151
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.072	0.000	0.073
bootstrapMI	0.288	0.000	0.287
bootstrapT	0.004	0.000	0.003
boxplot-methods	101.506	3.464	106.042
bracketMethods	0.272	0.020	0.289
calcA	0.160	0.104	0.265
calcW	0.160	0.108	0.267
classifyKNN	0.372	0.000	0.369
classifyKNNsc	0.6	0.0	0.6
classifyLDA	1.604	0.008	1.610
classifyLDAsc	2.836	0.004	2.871
classifySVM	0.820	0.068	1.146
classifySVMsc	1.380	0.012	1.505
coerce-methods	0.236	0.032	0.267
compCorr	0.000	0.000	0.001
createMaigesRaw	0.396	0.004	0.403
deGenes2by2BootT	0.777	0.004	0.779
deGenes2by2Ttest	0.360	0.008	0.373
deGenes2by2Wilcox	0.34	0.00	0.49
deGenesANOVA	0.444	0.000	0.444
designANOVA	0.132	0.004	0.135
dim-methods	0.072	0.000	0.071
getLabels	0.072	0.004	0.077
hierM	2.776	0.032	2.827
hierMde	0.596	0.004	0.620
image-methods	4.976	0.000	4.980
kmeansM	2.504	0.024	2.546
kmeansMde	0.640	0.000	0.642
loadData	0	0	0
normLoc	2.957	0.016	2.973
normOLIN	0.08	0.00	0.08
normRepLoess	0.072	0.004	0.074
normScaleLimma	82.465	2.528	85.006
normScaleMarray	60.887	1.452	62.386
plot-methods	11.425	0.084	11.705
plotGenePair	0.128	0.000	0.125
print-methods	0.172	0.008	0.181
relNet2TGF	0.180	0.000	0.183
relNetworkB	3.304	0.008	3.316
relNetworkM	0.116	0.000	0.117
robustCorr	0.000	0.000	0.001
selSpots	0.636	0.004	0.641
show-methods	0.173	0.008	0.179
somM	2.836	0.012	2.854
somMde	0.672	0.008	0.681
summarizeReplicates	4.192	0.028	4.293
summary-methods	0.172	0.016	0.193
tableClass	1.316	0.012	1.336
tablesDE	2.928	0.028	2.957