BioC 2.12: CHECK report for maigesPack on george2

Package: maigesPack

Version: 1.24.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.24.0.tar.gz

StartedAt: 2013-10-09 03:00:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:19:30 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 1134.8 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 3.0.1 (2013-05-16)
* 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 ‘1.24.0’
* 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 ... [13s/13s] 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 ... [16m/16m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
boxplot-methods    348.442  8.204 359.344
normScaleMarray    260.152  5.209 269.047
normScaleLimma     258.308  5.092 264.537
plot-methods        14.205  0.220  15.736
tablesDE             7.008  0.084   7.149
image-methods        7.056  0.028   7.089
activeNet            6.449  0.032   6.720
activeNetScoreHTML   6.464  0.016   6.573
* 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
** testing if installed package can be loaded
* DONE (maigesPack)

name	user	system	elapsed
MI	0.168	0.000	0.170
activeMod	3.844	0.036	4.006
activeModScoreHTML	1.940	0.012	1.964
activeNet	6.449	0.032	6.720
activeNetScoreHTML	6.464	0.016	6.573
addGeneGrps	0.024	0.000	0.026
addPaths	0.008	0.004	0.014
bootstrapCor	0.096	0.004	0.100
bootstrapMI	0.364	0.000	0.362
bootstrapT	0.028	0.004	0.033
boxplot-methods	348.442	8.204	359.344
bracketMethods	0.500	0.016	0.612
calcA	0.236	0.124	0.413
calcW	0.248	0.124	0.378
classifyKNN	0.360	0.008	0.420
classifyKNNsc	0.528	0.004	0.542
classifyLDA	1.644	0.016	1.667
classifyLDAsc	3.192	0.012	3.215
classifySVM	0.896	0.024	0.920
classifySVMsc	1.472	0.032	1.507
coerce-methods	0.204	0.044	0.248
compCorr	0.012	0.000	0.011
createMaigesRaw	0.744	0.012	0.760
deGenes2by2BootT	0.672	0.024	0.695
deGenes2by2Ttest	0.376	0.020	0.400
deGenes2by2Wilcox	0.336	0.008	0.347
deGenesANOVA	0.336	0.016	0.351
designANOVA	0.168	0.008	0.173
dim-methods	0.112	0.012	0.123
getLabels	0.108	0.008	0.113
hierM	2.205	0.028	2.243
hierMde	0.58	0.02	0.60
image-methods	7.056	0.028	7.089
kmeansM	2.648	0.040	2.687
kmeansMde	0.584	0.020	0.602
loadData	0.000	0.004	0.004
normLoc	4.177	0.008	4.188
normOLIN	0.096	0.008	0.104
normRepLoess	0.100	0.000	0.102
normScaleLimma	258.308	5.092	264.537
normScaleMarray	260.152	5.209	269.047
plot-methods	14.205	0.220	15.736
plotGenePair	0.160	0.012	0.172
print-methods	0.224	0.004	0.230
relNet2TGF	0.208	0.012	0.220
relNetworkB	3.052	0.012	3.084
relNetworkM	0.136	0.016	0.149
robustCorr	0.012	0.000	0.014
selSpots	0.548	0.024	0.572
show-methods	0.228	0.004	0.235
somM	2.660	0.028	2.697
somMde	0.628	0.020	0.646
summarizeReplicates	4.017	0.004	4.161
summary-methods	0.252	0.008	0.258
tableClass	1.632	0.004	1.639
tablesDE	7.008	0.084	7.149