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: 2013-03-25 02:50:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:07:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1044.8 seconds

RetCode: 0

Status:  OK

CheckDir: maigesPack.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/maigesPack.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ... [12s/12s] 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 ... [15m/15m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
boxplot-methods    350.278  9.060 367.607
normScaleLimma     255.564  5.216 267.969
normScaleMarray    152.057  3.133 158.526
plot-methods        15.657  0.140  16.634
tablesDE             7.569  0.096   7.861
image-methods        7.456  0.028   7.489
activeNet            6.973  0.012   6.987
activeNetScoreHTML   6.696  0.036   6.891
* 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
  ‘/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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -c stats.c -o stats.o
stats.c: In function ‘stats_median_from_sorted_data’:
stats.c:80:22: warning: operation on ‘i’ may be undefined [-Wsequence-point]
gcc -std=gnu99 -shared -L/usr/local/lib -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 /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	0.220	0.008	0.228
activeMod	4.096	0.044	4.139
activeModScoreHTML	2.284	0.004	2.286
activeNet	6.973	0.012	6.987
activeNetScoreHTML	6.696	0.036	6.891
addGeneGrps	0.008	0.004	0.012
addPaths	0.008	0.000	0.012
bootstrapCor	0.072	0.004	0.077
bootstrapMI	0.344	0.000	0.345
bootstrapT	0.02	0.00	0.02
boxplot-methods	350.278	9.060	367.607
bracketMethods	0.356	0.020	0.376
calcA	0.224	0.124	0.350
calcW	0.268	0.100	0.367
classifyKNN	0.564	0.016	0.578
classifyKNNsc	0.468	0.012	0.480
classifyLDA	1.624	0.000	1.624
classifyLDAsc	2.904	0.004	2.906
classifySVM	0.796	0.012	0.806
classifySVMsc	1.516	0.020	1.536
coerce-methods	0.228	0.020	0.249
compCorr	0.008	0.000	0.009
createMaigesRaw	0.469	0.000	0.470
deGenes2by2BootT	0.780	0.000	0.781
deGenes2by2Ttest	0.384	0.012	0.397
deGenes2by2Wilcox	0.636	0.020	0.658
deGenesANOVA	0.340	0.024	0.366
designANOVA	0.156	0.020	0.172
dim-methods	0.092	0.004	0.094
getLabels	0.100	0.012	0.108
hierM	2.080	0.032	2.116
hierMde	0.688	0.004	0.691
image-methods	7.456	0.028	7.489
kmeansM	2.797	0.028	2.827
kmeansMde	0.572	0.016	0.591
loadData	0.008	0.000	0.006
normLoc	3.992	0.004	4.088
normOLIN	0.080	0.004	0.086
normRepLoess	0.088	0.008	0.097
normScaleLimma	255.564	5.216	267.969
normScaleMarray	152.057	3.133	158.526
plot-methods	15.657	0.140	16.634
plotGenePair	0.168	0.012	0.179
print-methods	0.240	0.028	0.267
relNet2TGF	0.256	0.008	0.268
relNetworkB	4.221	0.044	4.581
relNetworkM	0.128	0.032	0.161
robustCorr	0.012	0.004	0.017
selSpots	0.600	0.012	0.661
show-methods	0.248	0.028	0.381
somM	2.864	0.040	3.161
somMde	0.716	0.012	0.729
summarizeReplicates	4.280	0.012	4.340
summary-methods	0.228	0.004	0.239
tableClass	1.392	0.004	1.399
tablesDE	7.569	0.096	7.861