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Package 158/479HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.5.0
David M. Schruth
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowPhyto
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  ERROR 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: flowPhyto
Version: 1.5.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.5.0.tar.gz
StartedAt: 2011-07-07 00:27:08 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 00:29:48 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 160.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowPhyto.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowPhyto’ can be installed ... WARNING
Found the following significant warnings:
  Warning: value of 'results' option should be lowercase
See ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowPhyto.Rcheck/00install.out’ for details.
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘flowPhyto.Rnw’ using ‘UTF-8’ 
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.DEF0.0120.0000.012
REPO.PATH0.0000.0000.001
census3.6120.0483.740
censusFile7.4240.4648.357
classify3.1610.0243.188
classifyFile1.0560.0081.066
cleanupLogs000
clearOutputs0.0080.0080.015
combineCensusFiles0.0160.0000.017
combineSdsFiles0.0160.0000.017
consensus2.0080.0042.011
consensusFile2.2520.0322.287
createResamplingScheme0.020.000.02
filter0.1400.0040.143
filterFile7.9080.8088.488
getCruiseFiles0.0040.0000.004
getCruisePath0.0040.0000.004
getFileNumber0.0040.0000.004
joinSDS0.220.000.22
pipeline0.0440.2040.252
plotCruiseStats14.949 1.08816.427
plotCytogram2.3280.0082.421
plotLatLongMap2.1280.1962.332
plotStatMap2.5600.1362.701
readConsensusFile0.0120.0000.010
readPopDef0.0080.0000.009
readSeaflow0.1120.0000.110
summarize1.7210.0241.749
summarizeFile1.3680.0081.382
validatePopDef0.0040.0040.005
writeSeaflow 0.136 0.00030.160