Package: flowPhyto

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.9.0.tar.gz

StartedAt: 2012-06-20 23:46:54 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:50:32 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 217.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowPhyto.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.9.0'
* 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 whether package 'flowPhyto' can be installed ... OK
* checking installed package size ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

* installing *source* package 'flowPhyto' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'flowPhyto.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0.000	0.000	0.001
CHANNEL.CLMNS.SM	0.001	0.000	0.000
EVT.HEADERS	0.001	0.000	0.000
POP.DEF	0.009	0.001	0.010
REPO.PATH	0	0	0
census	3.482	0.647	4.439
censusFile	5.848	0.705	7.903
classify	2.816	0.647	3.501
classifyFile	1.566	0.319	1.999
cleanupLogs	0.001	0.000	0.000
clearOutputs	0.010	0.031	0.063
combineCensusFiles	0.012	0.002	0.017
combineSdsFiles	0.015	0.003	0.018
consensus	1.912	0.022	1.945
consensusFile	1.946	0.049	2.082
createResamplingScheme	0.023	0.002	0.026
filter	0.176	0.020	0.197
filterFile	2.906	0.612	3.491
getCruiseFiles	0.003	0.002	0.005
getCruisePath	0.003	0.002	0.004
getFileNumber	0.003	0.002	0.005
joinSDS	0.255	0.029	0.286
pipeline	29.381	2.023	31.757
plotCruiseStats	9.323	2.383	11.714
plotCytogram	2.958	0.651	3.634
plotLatLongMap	1.658	0.372	2.055
plotStatMap	1.726	0.410	2.159
readConsensusFile	0.012	0.003	0.015
readPopDef	0.009	0.002	0.010
readSeaflow	0.128	0.010	0.138
summarize	1.993	0.336	2.345
summarizeFile	1.530	0.195	1.785
validatePopDef	0.004	0.002	0.007
writeSeaflow	0.147	0.020	30.169