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Package 153/467HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.4.0
David M. Schruth
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/flowPhyto
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: flowPhyto
Version: 1.4.0
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.4.0.tar.gz
StartedAt: 2011-10-20 14:14:49 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:17:59 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 189.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowPhyto.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/flowPhyto.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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' ... WARNING
Package vignette(s) without corresponding PDF:
   flowPhyto.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/flowPhyto.Rcheck/00check.log'
for details

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)
** help
*** installing help indices
** building package indices ...
Warning: value of 'results' option should be lowercase
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS000
CHANNEL.CLMNS.SM000
EVT.HEADERS000
POP.DEF0.020.000.01
REPO.PATH000
census3.110.003.13
censusFile 6.73 0.4310.84
classify4.780.034.81
classifyFile1.800.042.06
cleanupLogs000
clearOutputs0.000.020.20
combineCensusFiles0.010.000.02
combineSdsFiles0.020.000.02
consensus2.20.02.2
consensusFile1.810.032.05
createResamplingScheme0.020.000.01
filter0.140.000.14
filterFile3.610.344.47
getCruiseFiles000
getCruisePath000
getFileNumber0.010.000.02
joinSDS0.220.000.23
pipeline 0.05 0.0425.08
plotCruiseStats14.78 1.5616.67
plotCytogram2.30.02.3
plotLatLongMap2.670.403.08
plotStatMap2.780.473.32
readConsensusFile0.020.000.02
readPopDef000
readSeaflow0.120.000.12
summarize1.750.021.77
summarizeFile1.360.011.63
validatePopDef000
writeSeaflow 0.13 0.0030.12