BioC 3.0: CHECK report for maigesPack on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/maigesPack.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.30.0’
* 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 ... [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 ... NOTE
'library' or 'require' calls in package code:
  ‘OLIN’ ‘annotate’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
tablesDE: no visible global function definition for ‘setRepository’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/71s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normScaleLimma  11.712  0.436  12.218
plot-methods     7.561  0.164   9.132
boxplot-methods  5.625  0.380   6.142
* 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
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-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-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	0.000	0.005
activeMod	1.992	0.016	2.035
activeModScoreHTML	1.032	0.032	1.069
activeNet	3.820	0.036	3.926
activeNetScoreHTML	3.852	0.016	4.058
addGeneGrps	0.004	0.000	0.000
addPaths	0.000	0.000	0.001
bootstrapCor	0.044	0.000	0.044
bootstrapMI	0.244	0.004	0.252
bootstrapT	0.004	0.000	0.003
boxplot-methods	5.625	0.380	6.142
bracketMethods	0.180	0.004	0.187
calcA	0.172	0.072	0.244
calcW	0.152	0.100	0.250
classifyKNN	0.216	0.028	0.271
classifyKNNsc	0.272	0.032	0.316
classifyLDA	0.868	0.032	0.941
classifyLDAsc	1.536	0.032	1.584
classifySVM	0.560	0.048	0.630
classifySVMsc	0.848	0.016	0.877
coerce-methods	0.116	0.008	0.124
compCorr	0.004	0.000	0.001
createMaigesRaw	0.216	0.012	0.234
deGenes2by2BootT	0.444	0.012	0.461
deGenes2by2Ttest	0.256	0.008	0.270
deGenes2by2Wilcox	0.224	0.024	0.254
deGenesANOVA	0.196	0.032	0.237
designANOVA	0.104	0.008	0.119
dim-methods	0.068	0.004	0.070
getLabels	0.072	0.008	0.081
hierM	1.300	0.008	1.357
hierMde	0.380	0.032	0.433
image-methods	1.504	0.032	1.551
kmeansM	1.288	0.024	1.496
kmeansMde	0.408	0.012	0.454
loadData	0.000	0.000	0.001
normLoc	2.193	0.028	2.243
normOLIN	0.064	0.004	0.067
normRepLoess	0.064	0.004	0.068
normScaleLimma	11.712	0.436	12.218
normScaleMarray	2.900	0.208	3.122
plot-methods	7.561	0.164	9.132
plotGenePair	0.116	0.016	0.134
print-methods	0.160	0.004	0.164
relNet2TGF	0.152	0.012	0.175
relNetworkB	1.580	0.040	1.636
relNetworkM	0.096	0.012	0.113
robustCorr	0.004	0.000	0.002
selSpots	0.192	0.064	0.268
show-methods	0.108	0.028	0.139
somM	1.436	0.040	1.634
somMde	0.404	0.024	0.505
summarizeReplicates	1.788	0.064	1.865
summary-methods	0.152	0.004	0.165
tableClass	0.760	0.012	0.782
tablesDE	4.449	0.100	4.627

BioC 3.0: CHECK report for maigesPack on zin1

Summary

Command output