Package: flowPhyto

Version: 1.5.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.5.0.tar.gz

StartedAt: 2011-05-09 12:23:10 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:25:51 -0700 (Mon, 09 May 2011)

EllapsedTime: 160.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowPhyto.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘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 ... WARNING
Found the following significant warnings:
  Warning: value of 'results' option should be lowercase
See ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck/00install.out’ for details.
* 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 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

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck/00check.log’
for details

* 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	0.004	0.000	0.007
REPO.PATH	0	0	0
census	3.428	0.028	3.468
censusFile	7.560	0.404	8.280
classify	2.997	0.036	3.037
classifyFile	1.012	0.012	1.023
cleanupLogs	0	0	0
clearOutputs	0.004	0.008	0.013
combineCensusFiles	0.012	0.004	0.014
combineSdsFiles	0.028	0.000	0.028
consensus	1.928	0.000	1.926
consensusFile	1.952	0.000	1.953
createResamplingScheme	0.012	0.004	0.020
filter	0.140	0.000	0.142
filterFile	7.660	0.588	7.699
getCruiseFiles	0.000	0.004	0.004
getCruisePath	0.004	0.000	0.003
getFileNumber	0.004	0.000	0.003
joinSDS	0.212	0.000	0.212
pipeline	0.040	0.196	0.239
plotCruiseStats	16.125	0.812	16.793
plotCytogram	2.268	0.020	2.293
plotLatLongMap	2.404	0.056	2.460
plotStatMap	2.492	0.040	2.536
readConsensusFile	0.008	0.000	0.009
readPopDef	0.008	0.000	0.009
readSeaflow	0.109	0.000	0.108
summarize	1.540	0.004	1.575
summarizeFile	1.400	0.020	1.427
validatePopDef	0.004	0.000	0.005
writeSeaflow	0.140	0.004	30.173