BioC 3.1: CHECK report for maigesPack on zin2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/maigesPack.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.32.0’
* 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/7s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/81s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normScaleLimma  9.902  0.368  16.604
plot-methods    6.400  0.230   9.904
boxplot-methods 3.849  0.318   5.726
* 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-3.1-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.007
activeMod	1.583	0.027	2.138
activeModScoreHTML	0.823	0.017	1.624
activeNet	3.162	0.017	4.688
activeNetScoreHTML	3.144	0.020	4.322
addGeneGrps	0.000	0.000	0.001
addPaths	0.001	0.000	0.001
bootstrapCor	0.034	0.000	0.066
bootstrapMI	0.212	0.000	0.346
bootstrapT	0.003	0.000	0.003
boxplot-methods	3.849	0.318	5.726
bracketMethods	0.154	0.000	0.165
calcA	0.120	0.088	0.223
calcW	0.140	0.077	0.245
classifyKNN	0.173	0.030	0.294
classifyKNNsc	0.254	0.023	0.647
classifyLDA	0.697	0.037	1.281
classifyLDAsc	1.157	0.036	1.976
classifySVM	0.401	0.036	0.592
classifySVMsc	0.663	0.030	1.516
coerce-methods	0.099	0.012	0.138
compCorr	0.000	0.000	0.001
createMaigesRaw	0.206	0.014	0.275
deGenes2by2BootT	0.422	0.007	0.620
deGenes2by2Ttest	0.248	0.006	0.509
deGenes2by2Wilcox	0.213	0.022	0.304
deGenesANOVA	0.247	0.031	0.413
designANOVA	0.091	0.014	0.150
dim-methods	0.060	0.003	0.076
getLabels	0.062	0.012	0.076
hierM	1.069	0.027	1.513
hierMde	0.310	0.023	0.463
image-methods	1.196	0.030	1.581
kmeansM	1.127	0.027	1.289
kmeansMde	0.327	0.010	0.367
loadData	0.000	0.000	0.001
normLoc	2.170	0.024	2.720
normOLIN	0.067	0.000	0.144
normRepLoess	0.060	0.004	0.125
normScaleLimma	9.902	0.368	16.604
normScaleMarray	2.369	0.201	3.610
plot-methods	6.400	0.230	9.904
plotGenePair	0.092	0.021	0.196
print-methods	0.122	0.011	0.140
relNet2TGF	0.114	0.028	0.219
relNetworkB	1.432	0.060	2.237
relNetworkM	0.080	0.014	0.100
robustCorr	0.001	0.000	0.001
selSpots	0.176	0.042	0.293
show-methods	0.114	0.011	0.130
somM	1.286	0.019	1.558
somMde	0.348	0.023	0.696
summarizeReplicates	1.380	0.053	1.910
summary-methods	0.130	0.008	0.276
tableClass	0.539	0.023	0.665
tablesDE	2.814	0.058	4.093

BioC 3.1: CHECK report for maigesPack on zin2

Summary

Command output