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: 2011-07-07 01:16:25 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:28:34 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 729.3 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) (2011-06-15 r56138)
* 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	3.188	0.016	3.203
activeModScoreHTML	1.556	0.016	1.572
activeNet	4.944	0.000	4.954
activeNetScoreHTML	5.073	0.000	5.071
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.056	0.000	0.053
bootstrapMI	0.292	0.000	0.291
bootstrapT	0.004	0.000	0.004
boxplot-methods	221.589	4.476	228.056
bracketMethods	0.272	0.000	0.272
calcA	0.136	0.096	0.234
calcW	0.136	0.108	0.244
classifyKNN	0.300	0.000	0.322
classifyKNNsc	0.437	0.004	0.442
classifyLDA	1.684	0.004	1.688
classifyLDAsc	2.944	0.000	2.946
classifySVM	0.796	0.008	0.804
classifySVMsc	1.372	0.016	1.388
coerce-methods	0.280	0.024	0.307
compCorr	0	0	0
createMaigesRaw	0.408	0.012	0.438
deGenes2by2BootT	0.648	0.000	0.649
deGenes2by2Ttest	0.392	0.000	0.391
deGenes2by2Wilcox	0.320	0.004	0.326
deGenesANOVA	0.356	0.012	0.368
designANOVA	0.132	0.004	0.136
dim-methods	0.080	0.000	0.078
getLabels	0.084	0.004	0.089
hierM	2.432	0.020	2.453
hierMde	0.568	0.008	0.582
image-methods	5.641	0.012	5.649
kmeansM	2.560	0.016	2.576
kmeansMde	0.624	0.008	0.629
loadData	0	0	0
normLoc	3.096	0.004	3.097
normOLIN	0.076	0.000	0.076
normRepLoess	0.076	0.000	0.080
normScaleLimma	212.701	5.808	220.117
normScaleMarray	114.343	2.152	116.643
plot-methods	10.841	0.036	11.231
plotGenePair	0.120	0.000	0.121
print-methods	0.188	0.000	0.193
relNet2TGF	0.184	0.012	0.194
relNetworkB	2.964	0.008	2.978
relNetworkM	0.112	0.004	0.113
robustCorr	0.000	0.000	0.001
selSpots	0.684	0.008	0.690
show-methods	0.160	0.004	0.165
somM	2.589	0.016	2.665
somMde	0.528	0.012	0.539
summarizeReplicates	3.388	0.004	3.390
summary-methods	0.164	0.012	0.176
tableClass	1.276	0.000	1.274
tablesDE	2.932	0.012	2.947