BioC 2.14: CHECK report for maigesPack on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.28.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/maigesPack.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.28.1’
* 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 ... [6s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 files in ‘vignettes’ ... OK
* checking examples ... [66s/67s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normScaleLimma  11.864  0.408  12.337
plot-methods     7.749  0.036   8.124
boxplot-methods  5.769  0.456   6.234
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-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-2.14-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-2.14-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-2.14-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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stats.c -o stats.o
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-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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	0.004	0.004	0.005
activeMod	2.048	0.008	2.059
activeModScoreHTML	1.016	0.004	1.020
activeNet	3.800	0.008	3.814
activeNetScoreHTML	3.804	0.000	3.820
addGeneGrps	0	0	0
addPaths	0.004	0.000	0.001
bootstrapCor	0.036	0.000	0.036
bootstrapMI	0.248	0.000	0.246
bootstrapT	0.000	0.004	0.003
boxplot-methods	5.769	0.456	6.234
bracketMethods	0.184	0.004	0.186
calcA	0.176	0.064	0.240
calcW	0.188	0.060	0.247
classifyKNN	0.216	0.004	0.217
classifyKNNsc	0.268	0.000	0.269
classifyLDA	0.852	0.000	0.855
classifyLDAsc	1.640	0.000	1.644
classifySVM	0.476	0.016	0.490
classifySVMsc	0.776	0.012	0.788
coerce-methods	0.108	0.012	0.121
compCorr	0.004	0.000	0.000
createMaigesRaw	0.244	0.000	0.244
deGenes2by2BootT	0.436	0.004	0.440
deGenes2by2Ttest	0.268	0.000	0.266
deGenes2by2Wilcox	0.256	0.000	0.254
deGenesANOVA	0.196	0.004	0.198
designANOVA	0.168	0.004	0.175
dim-methods	0.064	0.000	0.065
getLabels	0.076	0.000	0.077
hierM	1.280	0.012	1.183
hierMde	0.360	0.008	0.370
image-methods	1.608	0.000	1.608
kmeansM	1.412	0.024	1.504
kmeansMde	0.356	0.000	0.355
loadData	0	0	0
normLoc	2.193	0.004	2.202
normOLIN	0.060	0.008	0.069
normRepLoess	0.064	0.004	0.069
normScaleLimma	11.864	0.408	12.337
normScaleMarray	2.356	0.136	2.494
plot-methods	7.749	0.036	8.124
plotGenePair	0.096	0.004	0.100
print-methods	0.132	0.004	0.137
relNet2TGF	0.132	0.000	0.133
relNetworkB	1.632	0.000	1.636
relNetworkM	0.088	0.004	0.089
robustCorr	0.000	0.000	0.001
selSpots	0.196	0.004	0.201
show-methods	0.136	0.004	0.141
somM	1.532	0.024	1.540
somMde	0.372	0.004	0.403
summarizeReplicates	1.656	0.004	1.665
summary-methods	0.144	0.000	0.144
tableClass	0.684	0.008	0.692
tablesDE	3.365	0.048	3.418

BioC 2.14: CHECK report for maigesPack on zin2

Summary

Command output