Package: maigesPack

Version: 1.17.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.17.0.tar.gz

StartedAt: 2011-05-09 13:07:30 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:21:26 -0700 (Mon, 09 May 2011)

EllapsedTime: 835.9 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/maigesPack.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.17.0’
* 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 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 ... 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 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/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c stats.c -o stats.o
stats.c: In function ‘stats_median_from_sorted_data’:
stats.c:80:22: warning: operation on ‘i’ may be undefined
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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-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
  'browseVignettes()'. 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 ...
*** tangling vignette sources ...
   ‘maigesPack_tutorial.Rnw’ 
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.004	0.000	0.004
activeMod	3.568	0.016	3.587
activeModScoreHTML	1.712	0.012	1.723
activeNet	5.156	0.004	5.228
activeNetScoreHTML	5.137	0.016	5.333
addGeneGrps	0	0	0
addPaths	0.000	0.000	0.001
bootstrapCor	0.052	0.000	0.052
bootstrapMI	0.3	0.0	0.3
bootstrapT	0.004	0.000	0.004
boxplot-methods	244.959	3.492	249.872
bracketMethods	0.368	0.008	0.377
calcA	0.164	0.080	0.245
calcW	0.176	0.080	0.257
classifyKNN	0.304	0.004	0.311
classifyKNNsc	0.444	0.004	0.448
classifyLDA	1.652	0.016	1.668
classifyLDAsc	3.040	0.000	3.132
classifySVM	0.780	0.000	0.779
classifySVMsc	1.400	0.000	1.398
coerce-methods	0.268	0.020	0.287
compCorr	0	0	0
createMaigesRaw	0.393	0.008	0.437
deGenes2by2BootT	0.624	0.000	0.627
deGenes2by2Ttest	0.380	0.000	0.379
deGenes2by2Wilcox	0.444	0.008	0.452
deGenesANOVA	0.352	0.000	0.350
designANOVA	0.128	0.008	0.137
dim-methods	0.080	0.000	0.077
getLabels	0.088	0.004	0.092
hierM	2.432	0.024	2.449
hierMde	0.612	0.016	0.690
image-methods	5.592	0.024	5.791
kmeansM	2.384	0.016	2.407
kmeansMde	0.572	0.000	0.603
loadData	0	0	0
normLoc	2.957	0.012	3.031
normOLIN	0.076	0.000	0.077
normRepLoess	0.068	0.004	0.073
normScaleLimma	270.096	4.108	276.019
normScaleMarray	137.385	2.788	141.619
plot-methods	10.793	0.060	11.112
plotGenePair	0.116	0.008	0.123
print-methods	0.176	0.004	0.180
relNet2TGF	0.180	0.000	0.179
relNetworkB	2.928	0.000	2.928
relNetworkM	0.120	0.000	0.117
robustCorr	0.000	0.000	0.001
selSpots	0.728	0.008	0.737
show-methods	0.168	0.004	0.172
somM	2.540	0.008	2.548
somMde	0.536	0.008	0.542
summarizeReplicates	3.632	0.008	3.643
summary-methods	0.188	0.000	0.188
tableClass	1.376	0.000	1.376
tablesDE	3.141	0.012	3.198