Package: flowPhyto

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.10.0.tar.gz

StartedAt: 2013-03-24 23:28:50 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:31:54 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 184.1 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 2.15.3 (2013-03-01)
* 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 '1.10.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        23.457  2.361  26.711
plotCruiseStats  7.380  2.432  10.001
censusFile       4.383  0.750   5.962
writeSeaflow     0.106  0.021  30.128
* 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	0.001	0.000	0.000
CHANNEL.CLMNS.SM	0	0	0
EVT.HEADERS	0.000	0.000	0.001
POP.DEF	0.008	0.002	0.018
REPO.PATH	0	0	0
census	2.611	0.659	3.549
censusFile	4.383	0.750	5.962
classify	2.056	0.663	2.816
classifyFile	0.942	0.300	1.326
cleanupLogs	0.001	0.001	0.001
clearOutputs	0.009	0.047	0.082
combineCensusFiles	0.009	0.003	0.015
combineSdsFiles	0.011	0.003	0.015
consensus	1.391	0.038	1.435
consensusFile	1.490	0.066	1.588
createResamplingScheme	0.018	0.002	0.022
filter	0.131	0.019	0.152
filterFile	2.183	0.698	2.965
getCruiseFiles	0.003	0.003	0.007
getCruisePath	0.002	0.002	0.004
getFileNumber	0.002	0.002	0.007
joinSDS	0.191	0.035	0.239
pipeline	23.457	2.361	26.711
plotCruiseStats	7.380	2.432	10.001
plotCytogram	1.894	0.636	2.626
plotLatLongMap	1.447	0.384	1.867
plotStatMap	1.283	0.377	1.701
readConsensusFile	0.010	0.004	0.014
readPopDef	0.007	0.003	0.010
readSeaflow	0.097	0.009	0.106
summarize	1.456	0.296	1.782
summarizeFile	1.067	0.215	1.319
validatePopDef	0.003	0.002	0.006
writeSeaflow	0.106	0.021	30.128