Package: maigesPack

Version: 1.21.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.21.2.tar.gz

StartedAt: 2012-06-21 01:23:15 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:35:07 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 711.7 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/maigesPack.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.21.2'
* 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-2.11-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	0.006
activeMod	4.225	0.067	4.423
activeModScoreHTML	2.099	0.047	2.288
activeNet	6.726	0.040	7.135
activeNetScoreHTML	6.634	0.032	6.745
addGeneGrps	0.001	0.000	0.001
addPaths	0.000	0.001	0.000
bootstrapCor	0.078	0.001	0.079
bootstrapMI	0.334	0.003	0.339
bootstrapT	0.005	0.001	0.006
boxplot-methods	134.879	44.960	189.932
bracketMethods	0.354	0.054	0.410
calcA	0.307	0.232	0.551
calcW	0.311	0.238	0.554
classifyKNN	0.410	0.024	0.456
classifyKNNsc	0.567	0.018	0.591
classifyLDA	1.854	0.030	1.905
classifyLDAsc	2.924	0.024	2.984
classifySVM	0.947	0.024	0.976
classifySVMsc	1.465	0.019	1.492
coerce-methods	0.231	0.079	0.310
compCorr	0.000	0.000	0.001
createMaigesRaw	0.562	0.030	0.596
deGenes2by2BootT	1.062	0.017	1.158
deGenes2by2Ttest	0.440	0.023	0.530
deGenes2by2Wilcox	0.397	0.016	0.464
deGenesANOVA	0.391	0.036	0.479
designANOVA	0.197	0.022	0.261
dim-methods	0.118	0.010	0.128
getLabels	0.126	0.021	0.146
hierM	2.380	0.222	2.632
hierMde	0.776	0.037	0.828
image-methods	6.126	3.754	10.523
kmeansM	2.717	0.222	2.968
kmeansMde	0.753	0.038	0.796
loadData	0.001	0.000	0.000
normLoc	4.139	0.444	4.750
normOLIN	0.124	0.012	0.135
normRepLoess	0.123	0.013	0.136
normScaleLimma	167.253	37.379	211.087
normScaleMarray	61.001	18.666	80.984
plot-methods	13.627	0.308	14.584
plotGenePair	0.188	0.025	0.216
print-methods	0.261	0.026	0.287
relNet2TGF	0.266	0.041	0.492
relNetworkB	3.426	0.079	3.546
relNetworkM	0.163	0.018	0.181
robustCorr	0.002	0.001	0.002
selSpots	0.526	0.164	0.698
show-methods	0.248	0.026	0.284
somM	3.116	0.277	3.422
somMde	0.750	0.039	0.794
summarizeReplicates	3.610	0.277	3.929
summary-methods	0.242	0.019	0.262
tableClass	1.401	0.021	1.433
tablesDE	4.679	0.105	4.834