Package: maigesPack

Version: 1.16.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.16.0.tar.gz

StartedAt: 2011-10-20 13:22:29 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:34:44 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 735.0 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.16.0’
* checking package namespace 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 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 ... 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-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
** 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	3.552	0.008	3.559
activeModScoreHTML	1.724	0.000	1.731
activeNet	5.188	0.000	5.192
activeNetScoreHTML	5.253	0.000	5.255
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.052	0.000	0.054
bootstrapMI	0.400	0.000	0.399
bootstrapT	0.004	0.000	0.004
boxplot-methods	210.765	6.020	221.687
bracketMethods	0.388	0.004	0.398
calcA	0.132	0.100	0.235
calcW	0.152	0.088	0.240
classifyKNN	0.292	0.004	0.297
classifyKNNsc	0.440	0.004	0.444
classifyLDA	1.576	0.000	1.579
classifyLDAsc	2.664	0.000	2.665
classifySVM	0.716	0.012	0.728
classifySVMsc	1.248	0.012	1.447
coerce-methods	0.264	0.016	0.279
compCorr	0	0	0
createMaigesRaw	0.368	0.012	0.386
deGenes2by2BootT	0.608	0.000	0.638
deGenes2by2Ttest	0.344	0.000	0.362
deGenes2by2Wilcox	0.304	0.004	0.313
deGenesANOVA	0.340	0.000	0.348
designANOVA	0.116	0.004	0.128
dim-methods	0.068	0.000	0.071
getLabels	0.076	0.008	0.085
hierM	2.401	0.012	2.670
hierMde	0.624	0.004	0.648
image-methods	5.440	0.000	5.458
kmeansM	2.344	0.024	2.379
kmeansMde	0.548	0.004	0.562
loadData	0	0	0
normLoc	3.080	0.004	3.321
normOLIN	0.068	0.004	0.082
normRepLoess	0.072	0.004	0.074
normScaleLimma	210.106	2.464	213.868
normScaleMarray	132.608	1.960	135.639
plot-methods	11.357	0.044	11.928
plotGenePair	0.124	0.000	0.130
print-methods	0.180	0.000	0.181
relNet2TGF	0.328	0.012	0.339
relNetworkB	2.852	0.004	2.859
relNetworkM	0.120	0.000	0.118
robustCorr	0.000	0.000	0.001
selSpots	0.576	0.004	0.579
show-methods	0.180	0.008	0.189
somM	2.876	0.020	2.894
somMde	0.644	0.000	0.647
summarizeReplicates	3.620	0.012	3.649
summary-methods	0.164	0.008	0.173
tableClass	1.308	0.004	1.313
tablesDE	3.121	0.016	3.147