Package: maigesPack

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.15.0.tar.gz

StartedAt: 2011-02-24 20:05:28 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:16:30 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 662.4 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.15.0’
* 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 ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘maigesPack’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Minfo.c -o Minfo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c bootstrapT.c -o bootstrapT.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register.c -o register.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c robustCorr.c -o robustCorr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c stats.c -o stats.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck/maigesPack/libs/i386
** 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 ...
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.006	0.000	0.006
activeMod	5.009	0.045	5.058
activeModScoreHTML	2.551	0.034	2.591
activeNet	7.622	0.040	7.664
activeNetScoreHTML	7.511	0.031	7.544
addGeneGrps	0.001	0.000	0.001
addPaths	0	0	0
bootstrapCor	0.089	0.001	0.090
bootstrapMI	0.373	0.002	0.376
bootstrapT	0.006	0.000	0.007
boxplot-methods	159.855	44.672	204.997
bracketMethods	0.474	0.052	0.526
calcA	0.416	0.223	0.640
calcW	0.354	0.224	0.577
classifyKNN	0.492	0.020	0.538
classifyKNNsc	0.685	0.014	0.698
classifyLDA	2.148	0.019	2.168
classifyLDAsc	4.005	0.020	4.028
classifySVM	1.172	0.022	1.208
classifySVMsc	1.870	0.016	1.888
coerce-methods	0.306	0.073	0.379
compCorr	0.001	0.000	0.000
createMaigesRaw	0.634	0.020	0.653
deGenes2by2BootT	1.260	0.017	1.278
deGenes2by2Ttest	0.588	0.010	0.598
deGenes2by2Wilcox	0.530	0.008	0.538
deGenesANOVA	0.545	0.026	0.571
designANOVA	0.244	0.015	0.260
dim-methods	0.237	0.009	0.247
getLabels	0.205	0.016	0.220
hierM	3.427	0.184	3.552
hierMde	0.835	0.021	0.857
image-methods	7.117	3.414	10.552
kmeansM	3.229	0.187	3.414
kmeansMde	0.814	0.017	0.833
loadData	0.000	0.000	0.001
normLoc	4.368	0.393	4.766
normOLIN	0.230	0.008	0.237
normRepLoess	0.159	0.005	0.163
normScaleLimma	139.086	32.236	171.769
normScaleMarray	57.994	16.191	74.351
plot-methods	16.038	0.276	16.849
plotGenePair	0.227	0.016	0.244
print-methods	0.314	0.015	0.331
relNet2TGF	0.313	0.028	0.355
relNetworkB	4.370	0.051	4.424
relNetworkM	0.211	0.014	0.225
robustCorr	0.001	0.000	0.002
selSpots	0.775	0.142	0.917
show-methods	0.397	0.017	0.413
somM	3.643	0.209	3.853
somMde	0.941	0.021	0.962
summarizeReplicates	4.726	0.245	4.977
summary-methods	0.305	0.012	0.318
tableClass	1.759	0.016	1.777
tablesDE	4.791	0.455	5.254