BioC 3.3: CHECK report for maigesPack on linux2.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.35.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/maigesPack.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.35.0’
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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’
Undefined global functions or variables:
  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 ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normScaleLimma 10.189  0.356  10.544
plot-methods    5.806  0.181   6.143
* 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

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.005	0.000	0.004
activeMod	1.402	0.019	1.421
activeModScoreHTML	0.660	0.040	0.701
activeNet	3.831	0.028	3.867
activeNetScoreHTML	2.939	0.010	2.951
addGeneGrps	0	0	0
addPaths	0.001	0.000	0.000
bootstrapCor	0.137	0.004	0.141
bootstrapMI	0.273	0.004	0.277
bootstrapT	0.005	0.000	0.005
boxplot-methods	3.767	0.372	4.146
bracketMethods	0.202	0.016	0.218
calcA	0.127	0.056	0.183
calcW	0.127	0.040	0.167
classifyKNN	0.234	0.016	0.249
classifyKNNsc	0.351	0.030	0.379
classifyLDA	0.885	0.042	0.927
classifyLDAsc	1.436	0.042	1.478
classifySVM	0.492	0.039	0.531
classifySVMsc	0.682	0.032	0.713
coerce-methods	0.137	0.012	0.148
compCorr	0.001	0.000	0.001
createMaigesRaw	0.205	0.008	0.214
deGenes2by2BootT	0.445	0.015	0.459
deGenes2by2Ttest	0.313	0.016	0.329
deGenes2by2Wilcox	0.376	0.028	0.403
deGenesANOVA	0.234	0.040	0.273
designANOVA	0.120	0.027	0.146
dim-methods	0.09	0.00	0.09
getLabels	0.071	0.016	0.088
hierM	1.344	0.008	1.203
hierMde	0.382	0.018	0.401
image-methods	1.594	0.029	1.627
kmeansM	1.334	0.028	1.347
kmeansMde	0.367	0.025	0.391
loadData	0.001	0.000	0.001
normLoc	2.230	0.035	2.270
normOLIN	0.086	0.000	0.087
normRepLoess	0.098	0.000	0.099
normScaleLimma	10.189	0.356	10.544
normScaleMarray	2.721	0.185	2.906
plot-methods	5.806	0.181	6.143
plotGenePair	0.080	0.024	0.104
print-methods	0.142	0.012	0.155
relNet2TGF	0.118	0.023	0.139
relNetworkB	1.746	0.052	1.800
relNetworkM	0.076	0.015	0.091
robustCorr	0.001	0.000	0.001
selSpots	0.159	0.060	0.219
show-methods	0.168	0.012	0.181
somM	1.545	0.020	1.556
somMde	0.349	0.034	0.382
summarizeReplicates	1.658	0.062	1.719
summary-methods	0.167	0.012	0.179
tableClass	0.519	0.017	0.535
tablesDE	2.970	0.083	3.052

BioC 3.3: CHECK report for maigesPack on linux2.bioconductor.org

Summary

Command output