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Package 171/514HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.6.0
David M. Schruth
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/flowPhyto
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: flowPhyto
Version: 1.6.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.6.0.tar.gz
StartedAt: 2012-03-24 00:19:58 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:22:31 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 153.9 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.6.0’
* 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 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 examples ... OK
* 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

flowPhyto.Rcheck/00install.out:

* installing *source* package ‘flowPhyto’ ...
** R
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import ‘.__C__character’ when loading ‘methods’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘flowPhyto.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
replacing previous import ‘.__C__character’ when loading ‘methods’ 

* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS000
CHANNEL.CLMNS.SM000
EVT.HEADERS000
POP.DEF0.0040.0040.006
REPO.PATH000
census2.9480.0363.014
censusFile7.5000.4528.155
classify2.8250.0402.881
classifyFile0.9760.0160.993
cleanupLogs0.0000.0000.001
clearOutputs0.0040.0120.015
combineCensusFiles0.0160.0000.015
combineSdsFiles0.0120.0040.012
consensus1.4480.0001.452
consensusFile1.5840.0081.590
createResamplingScheme0.0200.0040.024
filter0.1360.0040.142
filterFile3.5040.4124.039
getCruiseFiles0.0040.0000.004
getCruisePath0.0040.0000.003
getFileNumber0.0040.0000.003
joinSDS0.1760.0040.195
pipeline0.0400.2040.268
plotCruiseStats15.097 1.00416.336
plotCytogram1.9720.0201.995
plotLatLongMap2.6320.0882.717
plotStatMap2.8800.1803.082
readConsensusFile0.0040.0040.009
readPopDef0.0040.0040.007
readSeaflow0.0880.0000.089
summarize1.4880.0161.511
summarizeFile1.1050.0201.126
validatePopDef0.0000.0040.005
writeSeaflow 0.100 0.00030.124