Package: maigesPack

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.17.0.tar.gz

StartedAt: 2011-07-07 04:11:15 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:23:42 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 747.6 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/maigesPack.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
               old_size new_size compress
  gastro.RData    836Kb    460Kb       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 sizes of PDF files under 'inst/doc' ... 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Minfo.c -o Minfo.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c bootstrapT.c -o bootstrapT.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register.c -o register.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c robustCorr.c -o robustCorr.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c stats.c -o stats.o
gcc-4.2 -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-2.9-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 ...
*** tangling vignette sources ...
   'maigesPack_tutorial.Rnw' 
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.006	0.001	0.006
activeMod	4.793	0.063	4.955
activeModScoreHTML	2.434	0.048	2.607
activeNet	7.690	0.053	8.184
activeNetScoreHTML	7.695	0.052	8.570
addGeneGrps	0.000	0.001	0.000
addPaths	0	0	0
bootstrapCor	0.091	0.002	0.098
bootstrapMI	0.378	0.003	0.394
bootstrapT	0.005	0.000	0.005
boxplot-methods	133.931	47.337	189.106
bracketMethods	0.433	0.053	0.490
calcA	0.355	0.224	0.587
calcW	0.367	0.236	0.609
classifyKNN	0.495	0.017	0.535
classifyKNNsc	0.709	0.014	0.730
classifyLDA	2.365	0.027	2.407
classifyLDAsc	3.939	0.023	4.004
classifySVM	1.137	0.020	1.182
classifySVMsc	1.911	0.019	1.955
coerce-methods	0.375	0.082	0.468
compCorr	0	0	0
createMaigesRaw	0.636	0.017	0.658
deGenes2by2BootT	1.235	0.014	1.265
deGenes2by2Ttest	0.602	0.012	0.626
deGenes2by2Wilcox	0.616	0.014	0.631
deGenesANOVA	0.572	0.032	0.608
designANOVA	0.255	0.017	0.273
dim-methods	0.172	0.008	0.184
getLabels	0.177	0.016	0.196
hierM	3.463	0.223	3.674
hierMde	0.907	0.027	0.942
image-methods	7.033	3.588	10.873
kmeansM	3.432	0.213	3.892
kmeansMde	0.777	0.021	0.829
loadData	0.000	0.001	0.001
normLoc	4.732	0.436	5.931
normOLIN	0.171	0.007	0.179
normRepLoess	0.169	0.006	0.181
normScaleLimma	130.135	35.117	170.079
normScaleMarray	99.641	17.486	120.572
plot-methods	16.127	0.319	18.556
plotGenePair	0.241	0.017	0.384
print-methods	0.322	0.016	0.518
relNet2TGF	0.324	0.030	0.618
relNetworkB	4.562	0.066	5.387
relNetworkM	0.227	0.017	0.262
robustCorr	0.002	0.001	0.002
selSpots	0.816	0.143	0.970
show-methods	0.314	0.014	0.406
somM	4.014	0.271	5.311
somMde	0.959	0.028	1.254
summarizeReplicates	5.369	0.286	7.132
summary-methods	0.330	0.017	0.546
tableClass	1.956	0.020	2.010
tablesDE	4.098	0.472	5.304