BioC 2.13: CHECK report for flowPhyto on zin1

Package: flowPhyto

Version: 1.14.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.14.0.tar.gz

StartedAt: 2014-04-05 01:09:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:12:18 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 147.9 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/flowPhyto.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.0’
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘flowPhyto.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [49s/78s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        20.845  0.824  21.785
plotCruiseStats  5.281  0.244   5.244
writeSeaflow     0.068  0.000  30.101
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (flowPhyto)

name	user	system	elapsed
CHANNEL.CLMNS	0.000	0.004	0.003
CHANNEL.CLMNS.SM	0.000	0.000	0.003
EVT.HEADERS	0.004	0.000	0.003
POP.DEF	0.008	0.000	0.008
REPO.PATH	0.004	0.000	0.002
census	1.836	0.004	1.842
censusFile	3.656	0.248	3.744
classify	1.332	0.000	1.332
classifyFile	0.584	0.004	0.598
cleanupLogs	0.000	0.000	0.001
clearOutputs	0.000	0.008	0.011
cmdArgsToVariables	0.000	0.000	0.001
combineCensusFiles	0.008	0.000	0.010
combineSdsFiles	0.012	0.000	0.012
consensus	1.104	0.004	1.111
consensusFile	1.180	0.004	1.204
createResamplingScheme	0.020	0.000	0.019
filter	0.112	0.000	0.123
filterFile	1.780	0.268	1.888
getCruiseFiles	0.008	0.000	0.008
getCruisePath	0.008	0.000	0.004
getFileNumber	0.004	0.000	0.004
joinSDS	0.156	0.000	0.156
pipeline	20.845	0.824	21.785
plotCruiseStats	5.281	0.244	5.244
plotCytogram	1.320	0.008	1.327
plotLatLongMap	0.920	0.052	0.979
plotStatMap	0.896	0.020	0.919
readConsensusFile	0.012	0.000	0.011
readPopDef	0.008	0.000	0.008
readSeaflow	0.064	0.000	0.065
summarize	1.140	0.012	1.155
summarizeFile	0.864	0.008	0.873
validatePopDef	0.004	0.000	0.005
writeSeaflow	0.068	0.000	30.101