Package: flowPhyto

Version: 1.5.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings flowPhyto_1.5.0.tar.gz

StartedAt: 2011-05-09 16:47:17 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:51:17 -0700 (Mon, 09 May 2011)

EllapsedTime: 239.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/flowPhyto.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.5.0'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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'
.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'
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'
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 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

* installing *source* package 'flowPhyto' ...
** R
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'flowPhyto.Rnw' using 'UTF-8' 
Warning: value of 'results' option should be lowercase
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0	0	0
CHANNEL.CLMNS.SM	0	0	0
EVT.HEADERS	0	0	0
POP.DEF	0.02	0.00	0.01
REPO.PATH	0	0	0
census	2.89	0.00	2.89
censusFile	6.73	0.37	10.22
classify	4.83	0.05	4.89
classifyFile	1.82	0.02	2.05
cleanupLogs	0	0	0
clearOutputs	0.02	0.01	0.22
combineCensusFiles	0	0	0
combineSdsFiles	0.01	0.00	0.02
consensus	1.97	0.00	1.97
consensusFile	2.02	0.02	2.67
createResamplingScheme	0.01	0.00	0.01
filter	0.28	0.01	0.30
filterFile	3.81	0.39	4.81
getCruiseFiles	0	0	0
getCruisePath	0	0	0
getFileNumber	0.00	0.02	0.02
joinSDS	0.21	0.00	0.20
pipeline	0.07	0.00	24.17
plotCruiseStats	15.48	1.98	17.84
plotCytogram	2.20	0.07	2.35
plotLatLongMap	2.27	0.42	2.68
plotStatMap	2.47	0.31	2.86
readConsensusFile	0	0	0
readPopDef	0.02	0.00	0.01
readSeaflow	0.12	0.00	0.13
summarize	1.55	0.06	1.61
summarizeFile	1.42	0.02	1.65
validatePopDef	0	0	0
writeSeaflow	0.13	0.01	30.15