BioC 3.1: CHECK report for flowPhyto on zin2

Package: flowPhyto

Version: 1.19.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.19.0.tar.gz

StartedAt: 2014-11-17 01:02:13 -0800 (Mon, 17 Nov 2014)

EndedAt: 2014-11-17 01:06:25 -0800 (Mon, 17 Nov 2014)

EllapsedTime: 251.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/flowPhyto.Rcheck’
* using R Under development (unstable) (2014-11-03 r66928)
* 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 ‘1.19.0’
* 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 loading without being on the library search path ... 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 global function definition for ‘dbConnect’
.DBcon: no visible global function definition for ‘dbDriver’
.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’
.interpolateSDSLatLon: no visible global function definition for
  ‘na.approx’
.loadSDS: no visible global function definition for ‘dbReadTable’
.loadSDS: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadSDS: no visible global function definition for ‘dbGetQuery’
.loadSDS: no visible binding for global variable ‘.db.sds.tab.nm’
.loadSDS: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadSDS: no visible global function definition for ‘dbListFields’
.loadSDS: no visible global function definition for ‘dbWriteTable’
.loadStats: no visible global function definition for ‘dbReadTable’
.loadStats: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadStats: no visible global function definition for ‘dbGetQuery’
.loadStats: no visible binding for global variable ‘.db.stats.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadStats: no visible global function definition for ‘dbListFields’
.loadStats: no visible global function definition for ‘dbWriteTable’
.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’
plotLatLongMap: no visible global function definition for
  ‘color.legend’
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 files in ‘vignettes’ ... OK
* checking examples ... [151s/185s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotCytogram    12.017 26.495  39.919
classify        11.384 26.166  38.326
census          11.490 25.615  37.748
pipeline        17.243  1.231  18.976
plotCruiseStats  4.779  0.254   4.964
writeSeaflow     0.148  0.087  30.060
* 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
* DONE

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.1-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	0	0
CHANNEL.CLMNS.SM	0	0	0
EVT.HEADERS	0.000	0.000	0.001
POP.DEF	0.005	0.000	0.005
REPO.PATH	0.000	0.000	0.001
census	11.490	25.615	37.748
censusFile	2.949	0.223	3.243
classify	11.384	26.166	38.326
classifyFile	0.471	0.004	0.475
cleanupLogs	0.000	0.000	0.001
clearOutputs	0.005	0.003	0.010
cmdArgsToVariables	0.002	0.000	0.001
combineCensusFiles	0.010	0.000	0.011
combineSdsFiles	0.007	0.004	0.013
consensus	0.981	0.027	1.008
consensusFile	0.988	0.032	1.037
createResamplingScheme	0.016	0.000	0.016
filter	0.075	0.000	0.076
filterFile	1.563	0.211	1.807
getCruiseFiles	0.004	0.001	0.003
getCruisePath	0.004	0.000	0.003
getFileNumber	0.001	0.000	0.002
joinSDS	0.132	0.000	0.140
pipeline	17.243	1.231	18.976
plotCruiseStats	4.779	0.254	4.964
plotCytogram	12.017	26.495	39.919
plotLatLongMap	0.816	0.009	0.851
plotStatMap	0.920	0.003	1.031
readConsensusFile	0.003	0.006	0.011
readPopDef	0.006	0.000	0.007
readSeaflow	0.057	0.000	0.056
summarize	1.055	0.033	1.168
summarizeFile	0.732	0.012	0.744
validatePopDef	0.003	0.001	0.005
writeSeaflow	0.148	0.087	30.060