Package: flowPhyto

Version: 1.10.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.10.0.tar.gz

StartedAt: 2013-03-25 01:03:54 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:06:29 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 154.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/flowPhyto.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.10.0’
* 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 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 7.748  0.400   8.679
censusFile      5.016  0.232   6.323
writeSeaflow    0.084  0.004  30.117
* 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-2.11-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	0	0
CHANNEL.CLMNS.SM	0	0	0
EVT.HEADERS	0	0	0
POP.DEF	0.004	0.000	0.006
REPO.PATH	0.000	0.000	0.001
census	2.652	0.020	2.707
censusFile	5.016	0.232	6.323
classify	1.988	0.008	2.257
classifyFile	0.920	0.008	1.071
cleanupLogs	0	0	0
clearOutputs	0.008	0.004	0.013
combineCensusFiles	0.012	0.000	0.010
combineSdsFiles	0.008	0.004	0.013
consensus	1.316	0.008	1.327
consensusFile	1.333	0.012	1.356
createResamplingScheme	0.020	0.000	0.019
filter	0.156	0.000	0.161
filterFile	2.376	0.216	2.682
getCruiseFiles	0.000	0.004	0.004
getCruisePath	0.004	0.000	0.011
getFileNumber	0.004	0.000	0.003
joinSDS	0.196	0.000	0.197
pipeline	0.036	0.072	0.132
plotCruiseStats	7.748	0.400	8.679
plotCytogram	1.904	0.004	1.947
plotLatLongMap	1.212	0.076	1.362
plotStatMap	1.432	0.060	1.493
readConsensusFile	0.004	0.004	0.022
readPopDef	0.008	0.000	0.009
readSeaflow	0.080	0.004	0.086
summarize	1.329	0.012	1.494
summarizeFile	1.248	0.036	1.539
validatePopDef	0.004	0.000	0.004
writeSeaflow	0.084	0.004	30.117