Package: flowPhyto

Version: 1.11.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.11.0.tar.gz

StartedAt: 2013-01-16 02:28:44 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:31:14 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 150.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowPhyto.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.11.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowPhyto’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCruiseStats 8.440  0.556   9.015
censusFile      5.128  0.312   5.956
writeSeaflow    0.104  0.000  30.132
* 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
  ‘/loc/home/biocbuild/bbs-2.12-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	0.004	0.006
CHANNEL.CLMNS.SM	0.004	0.004	0.010
EVT.HEADERS	0.008	0.000	0.008
POP.DEF	0.008	0.004	0.012
REPO.PATH	0.008	0.000	0.006
census	2.852	0.016	2.868
censusFile	5.128	0.312	5.956
classify	2.028	0.008	2.035
classifyFile	1.120	0.004	1.127
cleanupLogs	0.004	0.000	0.004
clearOutputs	0.016	0.004	0.020
combineCensusFiles	0.016	0.000	0.016
combineSdsFiles	0.016	0.004	0.018
consensus	1.389	0.000	1.388
consensusFile	1.444	0.016	1.460
createResamplingScheme	0.016	0.004	0.023
filter	0.176	0.004	0.181
filterFile	2.460	0.272	2.743
getCruiseFiles	0.012	0.000	0.014
getCruisePath	0.008	0.000	0.008
getFileNumber	0.008	0.000	0.010
joinSDS	0.204	0.000	0.205
pipeline	0.040	0.100	0.155
plotCruiseStats	8.440	0.556	9.015
plotCytogram	2.004	0.020	2.025
plotLatLongMap	1.713	0.052	1.766
plotStatMap	1.484	0.072	1.560
readConsensusFile	0.016	0.000	0.017
readPopDef	0.016	0.000	0.015
readSeaflow	0.092	0.008	0.100
summarize	1.704	0.012	1.718
summarizeFile	1.376	0.020	1.397
validatePopDef	0.004	0.004	0.009
writeSeaflow	0.104	0.000	30.132