BioC 3.2: CHECK report for maigesPack on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/maigesPack.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.34.0’
* 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 ... [4s/4s] 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 ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normScaleLimma 10.932  0.359  11.288
plot-methods    6.532  0.226   7.221
* 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-3.2-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.003
activeMod	1.414	0.016	1.429
activeModScoreHTML	0.774	0.025	0.805
activeNet	3.166	0.015	3.177
activeNetScoreHTML	3.158	0.020	3.176
addGeneGrps	0	0	0
addPaths	0.001	0.000	0.001
bootstrapCor	0.032	0.004	0.036
bootstrapMI	0.201	0.000	0.201
bootstrapT	0.003	0.000	0.003
boxplot-methods	4.004	0.315	4.316
bracketMethods	0.140	0.008	0.148
calcA	0.148	0.052	0.200
calcW	0.137	0.072	0.209
classifyKNN	0.150	0.042	0.191
classifyKNNsc	0.238	0.027	0.264
classifyLDA	0.646	0.034	0.679
classifyLDAsc	1.095	0.030	1.151
classifySVM	0.372	0.026	0.397
classifySVMsc	0.617	0.024	0.641
coerce-methods	0.104	0.008	0.112
compCorr	0.001	0.000	0.000
createMaigesRaw	0.187	0.022	0.208
deGenes2by2BootT	0.466	0.021	0.487
deGenes2by2Ttest	0.221	0.015	0.235
deGenes2by2Wilcox	0.211	0.019	0.230
deGenesANOVA	0.164	0.032	0.196
designANOVA	0.093	0.014	0.106
dim-methods	0.064	0.004	0.065
getLabels	0.069	0.000	0.071
hierM	1.202	0.016	1.107
hierMde	1.438	0.043	1.479
image-methods	1.157	0.043	1.199
kmeansM	1.282	0.049	1.308
kmeansMde	0.317	0.019	0.336
loadData	0.000	0.004	0.000
normLoc	2.091	0.045	2.138
normOLIN	0.059	0.004	0.064
normRepLoess	0.061	0.000	0.061
normScaleLimma	10.932	0.359	11.288
normScaleMarray	2.834	0.201	3.033
plot-methods	6.532	0.226	7.221
plotGenePair	0.101	0.021	0.121
print-methods	0.126	0.000	0.127
relNet2TGF	0.122	0.025	0.148
relNetworkB	1.500	0.064	1.568
relNetworkM	0.094	0.029	0.122
robustCorr	0.001	0.001	0.002
selSpots	0.203	0.057	0.261
show-methods	0.131	0.016	0.146
somM	1.488	0.040	1.618
somMde	0.343	0.033	0.375
summarizeReplicates	1.453	0.075	1.528
summary-methods	0.133	0.016	0.149
tableClass	0.622	0.045	0.667
tablesDE	2.607	0.078	2.682

BioC 3.2: CHECK report for maigesPack on zin1

Summary

Command output