BioC 2.14: CHECK report for flowPhyto on zin2

Package: flowPhyto

Version: 1.16.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.16.0.tar.gz

StartedAt: 2014-10-07 23:36:04 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:38:26 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 142.3 seconds

RetCode: 0

Status:  OK

CheckDir: flowPhyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/flowPhyto.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.16.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [44s/74s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        18.405  0.712  19.639
plotCruiseStats  4.845  0.300   4.911
writeSeaflow     0.064  0.000  30.093
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-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	0.000	0.000	0.001
EVT.HEADERS	0	0	0
POP.DEF	0.108	0.000	0.110
REPO.PATH	0.000	0.000	0.001
census	1.516	0.004	1.520
censusFile	3.128	0.236	3.172
classify	1.400	0.032	1.518
classifyFile	0.764	0.176	0.998
cleanupLogs	0.004	0.000	0.001
clearOutputs	0.008	0.004	0.012
cmdArgsToVariables	0.000	0.004	0.001
combineCensusFiles	0.008	0.004	0.013
combineSdsFiles	0.016	0.000	0.016
consensus	1.156	0.012	1.169
consensusFile	1.096	0.012	1.119
createResamplingScheme	0.020	0.000	0.019
filter	0.084	0.000	0.085
filterFile	1.460	0.180	1.475
getCruiseFiles	0.004	0.000	0.004
getCruisePath	0.000	0.004	0.003
getFileNumber	0.004	0.000	0.003
joinSDS	0.144	0.000	0.154
pipeline	18.405	0.712	19.639
plotCruiseStats	4.845	0.300	4.911
plotCytogram	1.528	0.024	1.580
plotLatLongMap	0.928	0.040	0.989
plotStatMap	0.636	0.020	0.661
readConsensusFile	0.004	0.004	0.009
readPopDef	0.004	0.000	0.007
readSeaflow	0.056	0.000	0.056
summarize	0.948	0.004	0.954
summarizeFile	0.756	0.004	0.762
validatePopDef	0.004	0.000	0.004
writeSeaflow	0.064	0.000	30.093