Package: maigesPack

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.20.0.tar.gz

StartedAt: 2012-09-24 00:48:10 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:57:16 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 546.3 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/maigesPack.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.20.0'
* 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 ... 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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-2.10-bioc/meat/maigesPack.Rcheck/maigesPack/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'show' when loading 'limma'
** help
*** installing help indices
** building package indices
** installing vignettes
   'maigesPack_tutorial.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'show' when loading 'limma'

* DONE (maigesPack)

name	user	system	elapsed
MI	0.005	0.001	0.005
activeMod	3.776	0.043	3.825
activeModScoreHTML	1.598	0.032	1.635
activeNet	6.527	0.019	6.547
activeNetScoreHTML	7.295	0.018	7.319
addGeneGrps	0	0	0
addPaths	0.000	0.001	0.000
bootstrapCor	0.083	0.001	0.084
bootstrapMI	0.366	0.001	0.368
bootstrapT	0.006	0.000	0.006
boxplot-methods	128.160	32.343	161.517
bracketMethods	0.266	0.037	0.304
calcA	0.244	0.173	0.419
calcW	0.260	0.192	0.453
classifyKNN	0.340	0.018	0.359
classifyKNNsc	0.577	0.017	0.595
classifyLDA	1.684	0.022	1.708
classifyLDAsc	2.286	0.017	2.304
classifySVM	0.663	0.017	0.681
classifySVMsc	1.037	0.013	1.051
coerce-methods	0.171	0.052	0.225
compCorr	0	0	0
createMaigesRaw	0.407	0.019	0.426
deGenes2by2BootT	0.782	0.014	0.799
deGenes2by2Ttest	0.345	0.011	0.357
deGenes2by2Wilcox	0.308	0.010	0.322
deGenesANOVA	0.331	0.026	0.362
designANOVA	0.177	0.016	0.194
dim-methods	0.169	0.010	0.179
getLabels	0.101	0.014	0.115
hierM	1.903	0.142	1.994
hierMde	0.768	0.031	0.799
image-methods	4.733	2.534	7.298
kmeansM	2.114	0.137	2.241
kmeansMde	0.518	0.021	0.538
loadData	0	0	0
normLoc	2.795	0.281	3.089
normOLIN	0.094	0.007	0.101
normRepLoess	0.094	0.008	0.102
normScaleLimma	99.928	26.473	127.296
normScaleMarray	51.068	14.678	66.186
plot-methods	10.380	0.116	10.499
plotGenePair	0.152	0.018	0.175
print-methods	0.195	0.017	0.213
relNet2TGF	0.188	0.025	0.223
relNetworkB	2.686	0.044	2.737
relNetworkM	0.150	0.015	0.167
robustCorr	0.001	0.000	0.002
selSpots	0.525	0.152	0.680
show-methods	0.274	0.022	0.302
somM	2.461	0.218	2.680
somMde	0.630	0.025	0.654
summarizeReplicates	3.193	0.215	3.418
summary-methods	0.247	0.021	0.269
tableClass	1.277	0.017	1.295
tablesDE	4.055	0.097	4.156