Package: maigesPack

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.22.0.tar.gz

StartedAt: 2013-03-25 00:16:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:29:11 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 741.1 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 2.15.3 (2013-03-01)
* 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 '1.22.0'
* 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 for left-over 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
Examples with CPU or elapsed time > 5s
                      user system elapsed
normScaleLimma     199.665 37.812 244.533
boxplot-methods    169.133 47.222 227.685
normScaleMarray     65.983 17.384  86.116
plot-methods         9.793  0.337  10.499
image-methods        5.264  3.791   9.829
activeNet            4.983  0.027   5.061
tablesDE             4.853  0.148   5.123
activeNetScoreHTML   4.960  0.029   5.045
* 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 -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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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	0.003	0.001	0.004
activeMod	3.166	0.049	3.291
activeModScoreHTML	1.545	0.049	1.730
activeNet	4.983	0.027	5.061
activeNetScoreHTML	4.960	0.029	5.045
addGeneGrps	0.000	0.001	0.000
addPaths	0	0	0
bootstrapCor	0.059	0.002	0.062
bootstrapMI	0.223	0.003	0.228
bootstrapT	0.004	0.000	0.004
boxplot-methods	169.133	47.222	227.685
bracketMethods	0.264	0.051	0.320
calcA	0.230	0.180	0.428
calcW	0.245	0.190	0.444
classifyKNN	0.290	0.027	0.328
classifyKNNsc	0.416	0.019	0.440
classifyLDA	1.341	0.034	1.406
classifyLDAsc	2.079	0.024	2.138
classifySVM	0.621	0.025	0.665
classifySVMsc	1.062	0.021	1.110
coerce-methods	0.184	0.081	0.302
compCorr	0	0	0
createMaigesRaw	0.378	0.024	0.428
deGenes2by2BootT	0.767	0.020	0.794
deGenes2by2Ttest	0.316	0.015	0.337
deGenes2by2Wilcox	0.289	0.017	0.314
deGenesANOVA	0.285	0.034	0.321
designANOVA	0.148	0.021	0.171
dim-methods	0.092	0.012	0.105
getLabels	0.091	0.017	0.108
hierM	1.813	0.205	2.019
hierMde	0.538	0.037	0.583
image-methods	5.264	3.791	9.829
kmeansM	2.029	0.224	2.297
kmeansMde	0.491	0.038	0.552
loadData	0	0	0
normLoc	2.761	0.533	3.592
normOLIN	0.089	0.014	0.112
normRepLoess	0.091	0.015	0.120
normScaleLimma	199.665	37.812	244.533
normScaleMarray	65.983	17.384	86.116
plot-methods	9.793	0.337	10.499
plotGenePair	0.130	0.019	0.149
print-methods	0.176	0.017	0.193
relNet2TGF	0.177	0.038	0.248
relNetworkB	2.296	0.055	2.398
relNetworkM	0.117	0.015	0.133
robustCorr	0.001	0.000	0.001
selSpots	0.415	0.159	0.603
show-methods	0.175	0.020	0.206
somM	2.242	0.255	2.532
somMde	0.502	0.034	0.574
summarizeReplicates	2.650	0.277	3.052
summary-methods	0.194	0.021	0.226
tableClass	1.065	0.020	1.119
tablesDE	4.853	0.148	5.123