Package: maigesPack

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.18.0.tar.gz

StartedAt: 2012-03-24 02:15:55 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:29:04 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 789.8 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 2.14.2 (2012-02-29)
* 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 '1.18.0'
* 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 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 -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 -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 -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 -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 -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 -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
** 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	0.005	0.000	0.006
activeMod	4.165	0.046	4.256
activeModScoreHTML	2.159	0.039	2.258
activeNet	6.855	0.049	7.110
activeNetScoreHTML	6.779	0.031	6.943
addGeneGrps	0.000	0.000	0.001
addPaths	0	0	0
bootstrapCor	0.081	0.002	0.084
bootstrapMI	0.332	0.003	0.336
bootstrapT	0.005	0.001	0.006
boxplot-methods	154.039	47.594	211.000
bracketMethods	0.409	0.052	0.463
calcA	0.363	0.235	0.602
calcW	0.359	0.230	0.590
classifyKNN	0.445	0.021	0.488
classifyKNNsc	0.605	0.014	0.621
classifyLDA	1.925	0.022	1.952
classifyLDAsc	3.021	0.023	3.056
classifySVM	0.946	0.020	0.982
classifySVMsc	1.552	0.019	1.612
coerce-methods	0.271	0.072	0.350
compCorr	0.001	0.000	0.001
createMaigesRaw	0.598	0.023	0.634
deGenes2by2BootT	1.115	0.014	1.176
deGenes2by2Ttest	0.485	0.015	0.582
deGenes2by2Wilcox	0.438	0.010	0.456
deGenesANOVA	0.540	0.036	0.589
designANOVA	0.242	0.018	0.266
dim-methods	0.167	0.008	0.176
getLabels	0.171	0.015	0.186
hierM	3.126	0.231	3.419
hierMde	0.744	0.033	0.883
image-methods	6.141	3.718	10.826
kmeansM	3.027	0.239	3.308
kmeansMde	0.669	0.026	0.698
loadData	0.000	0.000	0.001
normLoc	4.641	0.429	5.443
normOLIN	0.169	0.010	0.198
normRepLoess	0.167	0.006	0.173
normScaleLimma	184.835	35.902	226.105
normScaleMarray	100.209	17.539	123.578
plot-methods	13.829	0.302	14.874
plotGenePair	0.232	0.019	0.251
print-methods	0.293	0.019	0.314
relNet2TGF	0.287	0.027	0.335
relNetworkB	3.267	0.058	3.342
relNetworkM	0.219	0.016	0.236
robustCorr	0.001	0.000	0.002
selSpots	0.581	0.153	0.741
show-methods	0.413	0.023	0.439
somM	3.415	0.271	3.724
somMde	0.777	0.029	0.811
summarizeReplicates	3.658	0.266	3.954
summary-methods	0.421	0.025	0.446
tableClass	1.458	0.013	1.479
tablesDE	4.743	0.091	4.881