BioC 2.12: CHECK report for flowPhyto on petty

Package: flowPhyto

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.12.1.tar.gz

StartedAt: 2013-10-08 22:22:23 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:27:02 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 279.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowPhyto.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowPhyto.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.12.1'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowPhyto' can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  'MASS' 'RSQLite' 'grid' 'sm'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.DBcon: no visible binding for global variable '.db.driver'
.DBcon: no visible binding for global variable '.db.user'
.DBcon: no visible binding for global variable '.db.pass'
.DBcon: no visible binding for global variable '.db.name'
.DBcon: no visible binding for global variable '.db.host'
.heatmap.2: no visible global function definition for 'invalid'
.heatmap.2: no visible global function definition for 'heatmap.2.key'
.loadSDS: no visible binding for global variable '.db.cruise.tab.nm'
.loadSDS: no visible binding for global variable '.db.sds.tab.nm'
.loadSDS: no visible binding for global variable '.db.cruise.fkey.nm'
.loadStats: no visible binding for global variable '.db.cruise.tab.nm'
.loadStats: no visible binding for global variable '.db.stats.tab.nm'
.loadStats: no visible binding for global variable '.db.cruise.fkey.nm'
.prePlotLevel2: no visible binding for global variable '.SOURCE.DIR'
.queryStats: no visible binding for global variable '.db.stats.tab.nm'
.queryStats: no visible binding for global variable
  '.db.cruise.fkey.nm'
.queryStats: no visible binding for global variable '.db.cruise.tab.nm'
classify: no visible binding for global variable 'pe'
classify: no visible binding for global variable 'chl_small'
classify: no visible binding for global variable 'fsc_perp'
classify: no visible binding for global variable 'fsc_small'
classify: no visible binding for global variable 'chl_big'
classify: no visible binding for global variable 'pop'
dbWriteTable2: no visible binding for global variable 'db.nchars'
filter: no visible binding for global variable 'D1'
filter: no visible binding for global variable 'D2'
filter: no visible binding for global variable 'fsc_small'
hyperplot: no visible binding for global variable 'out'
plotCruiseStats: no visible binding for global variable 'resamp'
plotCytogram: no visible binding for global variable 'pop'
spie: no visible global function definition for 'grid.newpage'
spie: no visible global function definition for 'pushViewport'
spie: no visible global function definition for 'viewport'
spie: no visible global function definition for 'grid.layout'
spie: no visible global function definition for 'dataViewport'
spie: no visible global function definition for 'grid.circle'
spie: no visible global function definition for 'gpar'
spie: no visible global function definition for 'grid.polygon'
spie: no visible global function definition for 'grid.rect'
spie: no visible global function definition for 'stringWidth'
spie: no visible global function definition for 'stringHeight'
spie: no visible global function definition for 'grid.text'
spie: no visible global function definition for 'grid.lines'
spie: no visible global function definition for 'unit'
spie: no visible global function definition for 'upViewport'
stats: no visible global function definition for 'recode'
summarize: no visible binding for global variable 'pop'
summarizeFile: no visible binding for global variable 'pop'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'addFactLevs' 'bestBy' 'cmdArgsToVariables' 'dbWriteTable2' 'delist'
  'geomean' 'groupBy' 'heatmatrix' 'hyperplot' 'labsegs' 'leghead' 'm'
  'makeElipseCoords' 'mvlabs' 'nerge' 'nv' 'pad' 'parseArgString' 'pct'
  'pies' 'plotClock' 'raAddArms' 'raAddAxLabs' 'raAddSigLines' 'raPlot'
  'read.tab' 'regroup' 'rerowname' 'spie' 'sstable' 'stats' 'tab2df'
  'textplot' 'usr2lims' 'vennMatrix' 'violins' 'wjitter' 'write.delim'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [99s/130s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        41.114  2.002  43.680
plotCruiseStats 10.409  1.050  11.237
censusFile       7.016  0.349   7.662
writeSeaflow     0.162  0.013  30.185
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

* installing *source* package 'flowPhyto' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0.008	0.000	0.009
CHANNEL.CLMNS.SM	0.004	0.000	0.004
EVT.HEADERS	0.007	0.001	0.008
POP.DEF	0.015	0.001	0.017
REPO.PATH	0.187	0.002	0.189
census	3.712	0.124	3.867
censusFile	7.016	0.349	7.662
classify	2.724	0.288	3.021
classifyFile	2.385	0.147	2.574
cleanupLogs	0.003	0.004	0.007
clearOutputs	0.015	0.030	0.051
combineCensusFiles	0.016	0.005	0.022
combineSdsFiles	0.021	0.006	0.029
consensus	2.224	0.019	2.268
consensusFile	2.270	0.038	2.355
createResamplingScheme	0.030	0.006	0.035
filter	0.193	0.011	0.204
filterFile	3.338	0.344	3.520
getCruiseFiles	0.014	0.016	0.030
getCruisePath	0.006	0.006	0.012
getFileNumber	0.007	0.005	0.012
joinSDS	0.299	0.016	0.317
pipeline	41.114	2.002	43.680
plotCruiseStats	10.409	1.050	11.237
plotCytogram	3.041	0.330	3.413
plotLatLongMap	1.762	0.265	2.046
plotStatMap	1.749	0.228	2.012
readConsensusFile	0.025	0.021	0.048
readPopDef	0.014	0.006	0.025
readSeaflow	0.144	0.010	0.160
summarize	2.352	0.090	2.518
summarizeFile	1.776	0.072	1.993
validatePopDef	0.008	0.006	0.016
writeSeaflow	0.162	0.013	30.185