Package: flowPhyto

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.6.0.tar.gz

StartedAt: 2012-03-24 00:59:14 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:03:14 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 239.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.6.0'
* 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 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 1.3-01)
Warning: replacing previous import '.__C__character' when loading 'methods'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'flowPhyto.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
replacing previous import '.__C__character' when loading 'methods' 

* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0.000	0.001	0.001
CHANNEL.CLMNS.SM	0	0	0
EVT.HEADERS	0.000	0.001	0.001
POP.DEF	0.009	0.001	0.010
REPO.PATH	0	0	0
census	3.637	0.667	4.809
censusFile	8.175	1.652	10.732
classify	4.344	0.963	5.378
classifyFile	1.378	0.324	1.764
cleanupLogs	0.001	0.000	0.001
clearOutputs	0.011	0.031	0.059
combineCensusFiles	0.013	0.003	0.024
combineSdsFiles	0.015	0.003	0.018
consensus	2.038	0.053	2.101
consensusFile	2.076	0.050	2.229
createResamplingScheme	0.024	0.001	0.028
filter	0.180	0.022	0.214
filterFile	4.539	1.610	6.149
getCruiseFiles	0.003	0.002	0.004
getCruisePath	0.003	0.001	0.003
getFileNumber	0.003	0.001	0.004
joinSDS	0.255	0.033	0.289
pipeline	29.447	2.109	32.641
plotCruiseStats	17.746	8.173	26.713
plotCytogram	2.911	0.741	4.009
plotLatLongMap	2.978	1.343	4.370
plotStatMap	3.584	1.380	5.052
readConsensusFile	0.012	0.004	0.015
readPopDef	0.008	0.002	0.010
readSeaflow	0.126	0.010	0.137
summarize	1.982	0.384	2.389
summarizeFile	1.522	0.208	1.782
validatePopDef	0.004	0.001	0.005
writeSeaflow	0.140	0.019	30.161