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: 2011-06-22 03:54:54 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 04:06:40 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 706.3 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) (2011-06-03 r56037)
* 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 ‘1.17.0’
* 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 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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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	0.009	0.001	0.010
activeMod	4.65	0.05	4.75
activeModScoreHTML	2.351	0.046	2.486
activeNet	7.214	0.053	7.535
activeNetScoreHTML	7.239	0.047	7.824
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.088	0.001	0.142
bootstrapMI	0.368	0.003	0.408
bootstrapT	0.006	0.001	0.006
boxplot-methods	150.295	47.117	206.560
bracketMethods	0.440	0.053	0.501
calcA	0.359	0.233	0.599
calcW	0.348	0.224	0.578
classifyKNN	0.481	0.021	0.535
classifyKNNsc	0.657	0.015	0.675
classifyLDA	2.212	0.020	2.251
classifyLDAsc	3.886	0.023	3.928
classifySVM	1.180	0.022	1.243
classifySVMsc	1.798	0.015	1.823
coerce-methods	0.299	0.073	0.374
compCorr	0.000	0.000	0.001
createMaigesRaw	0.627	0.019	0.650
deGenes2by2BootT	1.250	0.015	1.276
deGenes2by2Ttest	0.582	0.011	0.594
deGenes2by2Wilcox	0.531	0.012	0.546
deGenesANOVA	0.559	0.033	0.595
designANOVA	0.251	0.017	0.273
dim-methods	0.165	0.007	0.173
getLabels	0.210	0.016	0.228
hierM	3.380	0.216	3.721
hierMde	0.901	0.033	1.048
image-methods	6.804	3.450	11.353
kmeansM	3.158	0.198	3.471
kmeansMde	0.753	0.018	0.816
loadData	0.000	0.000	0.001
normLoc	4.363	0.418	4.860
normOLIN	0.163	0.007	0.170
normRepLoess	0.167	0.009	0.210
normScaleLimma	131.815	34.331	170.460
normScaleMarray	61.664	17.208	82.036
plot-methods	15.486	0.299	19.248
plotGenePair	0.234	0.017	0.333
print-methods	0.312	0.014	0.361
relNet2TGF	0.311	0.027	0.861
relNetworkB	4.380	0.070	4.612
relNetworkM	0.222	0.016	0.239
robustCorr	0.001	0.000	0.002
selSpots	0.799	0.150	0.986
show-methods	0.307	0.014	0.363
somM	3.968	0.271	5.148
somMde	0.879	0.027	0.911
summarizeReplicates	4.685	0.245	4.987
summary-methods	0.316	0.016	0.338
tableClass	1.807	0.018	1.927
tablesDE	4.832	0.480	5.396