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Package 139/436HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 0.99.7
David M. Schruth
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowPhyto
Last Changed Rev: 51660 / Revision: 53255
Last Changed Date: 2010-12-21 13:44:05 -0800 (Tue, 21 Dec 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  ERROR  OK 

Summary

Package: flowPhyto
Version: 0.99.7
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_0.99.7.tar.gz
StartedAt: 2011-02-24 19:11:51 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:14:08 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 136.8 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/flowPhyto.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPhyto/DESCRIPTION’ ... OK
* this is package ‘flowPhyto’ version ‘0.99.7’
* 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 ... 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’
.getSDS: no visible global function definition for ‘pad’
.getSDS: no visible binding for global variable ‘computerUTC’
.loadSDS: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadSDS: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadSDS: no visible binding for global variable ‘.db.sds.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadStats: no visible binding for global variable ‘.db.stats.tab.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’
.queueLimitCheck: no visible binding for global variable ‘queue.limit’
.queueLimitCheck: no visible global function definition for ‘Sys.wait’
.setYearDay: no visible global function definition for ‘pad’
classify: no visible binding for global variable ‘chl_small’
classify: no visible binding for global variable ‘pe’
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’
filter: no visible binding for global variable ‘D1dFSC’
filter: no visible binding for global variable ‘D2dFSC’
filter: no visible binding for global variable ‘D1’
filter: no visible binding for global variable ‘fsc_small’
filter: no visible binding for global variable ‘D2’
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 package vignettes in ‘inst/doc’ ... 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 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS000
EVT.HEADERS0.0010.0010.001
POP.DEF0.0110.0020.013
REPO.PATH0.0000.0000.001
census0.3620.0530.416
censusFile13.281 1.10913.872
classify2.0150.2612.361
classifyFile0.6790.1740.856
cleanupLogs0.0010.0000.001
clearOutputs0.0100.0250.034
combineCensusFiles0.0180.0020.021
combineSdsFiles0.0240.0020.027
consensus2.6180.0142.633
consensusFile2.7660.0432.825
createResamplingScheme0.0290.0010.030
filter0.0490.0150.063
filterFile20.028 1.77221.503
getCruiseFiles0.0040.0010.006
getCruisePath0.0030.0010.005
getFileNumber0.0030.0010.004
joinSDS0.0690.0200.125
pipeline1.1890.3002.180
plotCruiseStats12.618 1.65213.653
plotCytogram0.4880.1160.609
plotLatLongMap0.5590.1040.666
plotStatMap0.4790.1070.588
readConsensusFile0.0140.0030.017
readPopDef0.0120.0010.013
readSeaflow0.0130.0070.019
summarize0.5870.1780.774
summarizeFile0.1880.0880.279
validatePopDef0.0050.0010.007
writeSeaflow0.0240.0150.039