Package: maigesPack

Version: 1.18.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.18.0.tar.gz

StartedAt: 2012-03-24 01:18:33 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:28:48 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 615.5 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 2.14.2 (2012-02-29)
* 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 ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  gastro.RData    836Kb    459Kb       xz
* 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 compiled code ... 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 -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 -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 -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 -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 -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-2.9-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
** 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	2.904	0.012	2.915
activeModScoreHTML	1.432	0.004	1.443
activeNet	4.976	0.012	4.998
activeNetScoreHTML	4.588	0.008	4.737
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.044	0.000	0.045
bootstrapMI	0.277	0.004	0.277
bootstrapT	0.008	0.000	0.008
boxplot-methods	183.939	5.988	193.627
bracketMethods	0.256	0.004	0.265
calcA	0.188	0.064	0.254
calcW	0.184	0.088	0.271
classifyKNN	0.296	0.000	0.297
classifyKNNsc	0.420	0.004	0.421
classifyLDA	1.392	0.008	1.404
classifyLDAsc	2.464	0.000	2.469
classifySVM	0.716	0.004	0.722
classifySVMsc	1.212	0.004	1.220
coerce-methods	0.332	0.024	0.356
compCorr	0.000	0.000	0.001
createMaigesRaw	0.381	0.012	0.392
deGenes2by2BootT	0.548	0.004	0.554
deGenes2by2Ttest	0.280	0.008	0.288
deGenes2by2Wilcox	0.264	0.000	0.265
deGenesANOVA	0.304	0.012	0.319
designANOVA	0.124	0.008	0.139
dim-methods	0.072	0.000	0.074
getLabels	0.084	0.004	0.093
hierM	2.284	0.044	2.400
hierMde	0.456	0.012	0.467
image-methods	4.832	0.016	4.850
kmeansM	2.392	0.032	2.430
kmeansMde	0.412	0.008	0.425
loadData	0	0	0
normLoc	2.820	0.012	2.830
normOLIN	0.080	0.000	0.079
normRepLoess	0.076	0.000	0.074
normScaleLimma	196.001	4.716	202.094
normScaleMarray	65.532	0.856	66.556
plot-methods	9.484	0.060	9.741
plotGenePair	0.120	0.000	0.122
print-methods	0.192	0.000	0.195
relNet2TGF	0.148	0.000	0.153
relNetworkB	2.249	0.012	2.287
relNetworkM	0.100	0.000	0.105
robustCorr	0	0	0
selSpots	0.368	0.012	0.386
show-methods	0.188	0.008	0.201
somM	2.316	0.028	2.407
somMde	0.456	0.008	0.488
summarizeReplicates	2.604	0.000	2.618
summary-methods	0.188	0.008	0.196
tableClass	1.144	0.004	1.149
tablesDE	3.920	0.016	3.984