Package: flowPhyto

Version: 0.99.7

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_0.99.7.tar.gz

StartedAt: 2011-02-24 19:27:32 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:28:54 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 81.9 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/flowPhyto.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPhyto/DESCRIPTION’ ... OK
* this is package ‘flowPhyto’ version ‘0.99.7’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowPhyto’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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’
.getSDS: no visible global function definition for ‘pad’
.getSDS: no visible binding for global variable ‘computerUTC’
.loadSDS: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadSDS: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadSDS: no visible binding for global variable ‘.db.sds.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadStats: no visible binding for global variable ‘.db.stats.tab.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’
.queueLimitCheck: no visible binding for global variable ‘queue.limit’
.queueLimitCheck: no visible global function definition for ‘Sys.wait’
.setYearDay: no visible global function definition for ‘pad’
classify: no visible binding for global variable ‘chl_small’
classify: no visible binding for global variable ‘pe’
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’
filter: no visible binding for global variable ‘D1dFSC’
filter: no visible binding for global variable ‘D2dFSC’
filter: no visible binding for global variable ‘D1’
filter: no visible binding for global variable ‘fsc_small’
filter: no visible binding for global variable ‘D2’
plotCruiseStats: no visible binding for global variable ‘resamp’
plotCytogram: no visible binding for global variable ‘pop’
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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘flowPhyto’ ...
** R
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0	0	0
EVT.HEADERS	0	0	0
POP.DEF	0.004	0.004	0.008
REPO.PATH	0	0	0
census	0.440	0.004	0.444
censusFile	6.992	0.276	7.783
classify	1.220	0.016	1.241
classifyFile	0.508	0.016	0.526
cleanupLogs	0	0	0
clearOutputs	0.004	0.012	0.018
combineCensusFiles	0.012	0.000	0.012
combineSdsFiles	0.016	0.000	0.014
consensus	1.708	0.000	1.713
consensusFile	1.808	0.020	1.828
createResamplingScheme	0.020	0.000	0.019
filter	0.048	0.000	0.050
filterFile	5.016	0.512	4.882
getCruiseFiles	0.004	0.000	0.003
getCruisePath	0.004	0.000	0.002
getFileNumber	0.004	0.000	0.003
joinSDS	0.176	0.000	0.192
pipeline	0.688	0.148	1.504
plotCruiseStats	7.073	0.292	5.682
plotCytogram	0.288	0.004	0.294
plotLatLongMap	0.384	0.016	0.397
plotStatMap	0.372	0.020	0.393
readConsensusFile	0.008	0.000	0.009
readPopDef	0.008	0.000	0.008
readSeaflow	0.008	0.004	0.012
summarize	0.432	0.004	0.434
summarizeFile	0.124	0.024	0.158
validatePopDef	0.004	0.000	0.004
writeSeaflow	0.016	0.000	0.016