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: 2011-04-07 07:28:27 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:37:58 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 570.9 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	3.420	0.016	3.436
activeModScoreHTML	1.680	0.004	1.684
activeNet	4.908	0.000	4.907
activeNetScoreHTML	4.917	0.000	4.913
addGeneGrps	0	0	0
addPaths	0.000	0.000	0.001
bootstrapCor	0.056	0.000	0.055
bootstrapMI	0.280	0.000	0.278
bootstrapT	0.004	0.000	0.003
boxplot-methods	180.491	3.996	184.531
bracketMethods	0.328	0.008	0.337
calcA	0.132	0.136	0.267
calcW	0.176	0.104	0.279
classifyKNN	0.268	0.004	0.272
classifyKNNsc	0.388	0.004	0.390
classifyLDA	1.416	0.004	1.420
classifyLDAsc	2.632	0.000	2.633
classifySVM	0.660	0.000	0.658
classifySVMsc	1.112	0.004	1.113
coerce-methods	0.144	0.020	0.167
compCorr	0.000	0.000	0.001
createMaigesRaw	0.368	0.004	0.378
deGenes2by2BootT	0.580	0.008	0.588
deGenes2by2Ttest	0.344	0.000	0.346
deGenes2by2Wilcox	0.404	0.004	0.759
deGenesANOVA	0.308	0.008	0.315
designANOVA	0.116	0.008	0.124
dim-methods	0.068	0.004	0.071
getLabels	0.080	0.000	0.081
hierM	2.293	0.048	2.328
hierMde	0.564	0.004	0.567
image-methods	4.856	0.012	4.872
kmeansM	2.152	0.008	2.180
kmeansMde	0.488	0.004	0.493
loadData	0	0	0
normLoc	2.916	0.008	2.920
normOLIN	0.064	0.004	0.069
normRepLoess	0.068	0.000	0.067
normScaleLimma	104.979	4.892	109.904
normScaleMarray	128.896	0.696	129.749
plot-methods	10.449	0.056	10.625
plotGenePair	0.108	0.000	0.110
print-methods	0.160	0.000	0.163
relNet2TGF	0.164	0.000	0.164
relNetworkB	2.988	0.004	2.993
relNetworkM	0.108	0.000	0.105
robustCorr	0.000	0.000	0.001
selSpots	0.636	0.004	0.638
show-methods	0.156	0.004	0.161
somM	2.304	0.008	2.316
somMde	0.644	0.004	0.648
summarizeReplicates	3.236	0.008	3.243
summary-methods	0.164	0.000	0.164
tableClass	1.152	0.004	1.154
tablesDE	2.704	0.020	2.722