Package: maigesPack

Version: 1.23.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.23.0.tar.gz

StartedAt: 2013-01-16 04:03:31 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:12:21 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 529.9 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/maigesPack.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.23.0’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maigesPack’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
normScaleLimma     148.589  1.912 151.113
boxplot-methods    130.040  3.420 133.684
normScaleMarray     70.345  1.448  71.917
plot-methods        10.173  0.080  10.420
tablesDE             5.277  0.068   5.362
activeNet            5.160  0.012   5.173
image-methods        5.157  0.012   5.167
activeNetScoreHTML   5.013  0.008   5.019
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘maigesPack_tutorial.Rnw’ 
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.012	0.004	0.015
activeMod	3.092	0.032	3.164
activeModScoreHTML	1.584	0.008	1.591
activeNet	5.160	0.012	5.173
activeNetScoreHTML	5.013	0.008	5.019
addGeneGrps	0.004	0.000	0.006
addPaths	0.012	0.000	0.011
bootstrapCor	0.056	0.004	0.063
bootstrapMI	0.444	0.000	0.444
bootstrapT	0.008	0.000	0.009
boxplot-methods	130.040	3.420	133.684
bracketMethods	0.208	0.016	0.224
calcA	0.136	0.104	0.239
calcW	0.160	0.104	0.265
classifyKNN	0.264	0.004	0.299
classifyKNNsc	0.408	0.008	0.425
classifyLDA	1.276	0.004	1.295
classifyLDAsc	2.308	0.008	2.353
classifySVM	0.652	0.020	0.680
classifySVMsc	1.120	0.008	1.513
coerce-methods	0.360	0.012	0.369
compCorr	0.000	0.004	0.004
createMaigesRaw	0.344	0.012	0.357
deGenes2by2BootT	0.560	0.020	0.576
deGenes2by2Ttest	0.292	0.000	0.293
deGenes2by2Wilcox	0.268	0.008	0.273
deGenesANOVA	0.248	0.000	0.245
designANOVA	0.120	0.012	0.133
dim-methods	0.080	0.000	0.079
getLabels	0.076	0.012	0.086
hierM	1.680	0.008	1.682
hierMde	0.48	0.02	0.50
image-methods	5.157	0.012	5.167
kmeansM	2.084	0.044	2.171
kmeansMde	0.496	0.012	0.589
loadData	0.008	0.000	0.006
normLoc	3.716	0.004	3.792
normOLIN	0.084	0.004	0.095
normRepLoess	0.088	0.000	0.091
normScaleLimma	148.589	1.912	151.113
normScaleMarray	70.345	1.448	71.917
plot-methods	10.173	0.080	10.420
plotGenePair	0.124	0.004	0.129
print-methods	0.188	0.000	0.189
relNet2TGF	0.388	0.016	0.404
relNetworkB	2.352	0.024	2.374
relNetworkM	0.112	0.012	0.125
robustCorr	0.008	0.004	0.012
selSpots	0.396	0.020	0.415
show-methods	0.184	0.008	0.194
somM	2.348	0.012	2.360
somMde	0.460	0.008	0.467
summarizeReplicates	2.760	0.008	2.770
summary-methods	0.164	0.008	0.172
tableClass	1.120	0.004	1.124
tablesDE	5.277	0.068	5.362