Package: maigesPack

Version: 1.14.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.14.0.tar.gz

StartedAt: 2011-03-31 07:02:37 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:12:07 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 570.0 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/maigesPack.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.14.0’
* 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 for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-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	3.400	0.020	3.425
activeModScoreHTML	1.672	0.012	1.685
activeNet	4.876	0.008	4.883
activeNetScoreHTML	4.881	0.000	4.879
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.052	0.000	0.054
bootstrapMI	0.280	0.000	0.278
bootstrapT	0.004	0.000	0.003
boxplot-methods	180.487	3.384	183.979
bracketMethods	0.328	0.008	0.337
calcA	0.152	0.116	0.266
calcW	0.156	0.124	0.281
classifyKNN	0.264	0.012	0.303
classifyKNNsc	0.396	0.000	0.394
classifyLDA	1.424	0.012	1.435
classifyLDAsc	2.636	0.000	2.637
classifySVM	0.648	0.004	0.656
classifySVMsc	1.096	0.004	1.102
coerce-methods	0.152	0.012	0.164
compCorr	0	0	0
createMaigesRaw	0.368	0.000	0.379
deGenes2by2BootT	0.592	0.000	0.592
deGenes2by2Ttest	0.344	0.004	0.346
deGenes2by2Wilcox	0.396	0.004	0.399
deGenesANOVA	0.312	0.004	0.318
designANOVA	0.120	0.004	0.123
dim-methods	0.072	0.004	0.074
getLabels	0.076	0.004	0.082
hierM	2.273	0.040	2.302
hierMde	0.552	0.016	0.566
image-methods	4.856	0.008	4.867
kmeansM	2.152	0.004	2.182
kmeansMde	0.504	0.000	0.503
loadData	0	0	0
normLoc	2.936	0.024	3.022
normOLIN	0.064	0.004	0.069
normRepLoess	0.068	0.000	0.068
normScaleLimma	105.523	4.104	109.819
normScaleMarray	128.760	0.740	129.542
plot-methods	10.469	0.084	10.670
plotGenePair	0.116	0.000	0.117
print-methods	0.160	0.004	0.166
relNet2TGF	0.164	0.000	0.164
relNetworkB	3.000	0.000	3.007
relNetworkM	0.100	0.004	0.105
robustCorr	0.000	0.000	0.001
selSpots	0.628	0.004	0.633
show-methods	0.148	0.012	0.161
somM	2.304	0.020	2.340
somMde	0.648	0.000	0.650
summarizeReplicates	3.224	0.008	3.232
summary-methods	0.160	0.004	0.165
tableClass	1.148	0.008	1.154
tablesDE	2.741	0.020	2.772