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Package 187/553HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.8.0
David M. Schruth
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/flowPhyto
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: flowPhyto
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.8.0.tar.gz
StartedAt: 2012-09-24 00:06:07 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:09:18 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 191.2 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/flowPhyto.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.8.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

flowPhyto.Rcheck/00install.out:

* installing *source* package 'flowPhyto' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'flowPhyto.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS0.0010.0010.000
CHANNEL.CLMNS.SM0.0010.0000.000
EVT.HEADERS0.0000.0010.000
POP.DEF0.0100.0010.012
REPO.PATH0.0000.0000.001
census3.2850.5663.882
censusFile4.6830.5766.336
classify2.1420.5012.653
classifyFile1.3160.2701.599
cleanupLogs000
clearOutputs0.0090.0310.044
combineCensusFiles0.0100.0020.013
combineSdsFiles0.0110.0020.014
consensus1.5000.0191.520
consensusFile1.5510.0421.607
createResamplingScheme0.0230.0020.025
filter0.1370.0140.151
filterFile2.2770.4882.574
getCruiseFiles0.0030.0020.006
getCruisePath0.0010.0020.003
getFileNumber0.0030.0020.005
joinSDS0.2730.0270.301
pipeline23.664 1.67325.480
plotCruiseStats6.7251.8418.318
plotCytogram2.6430.5873.243
plotLatLongMap1.3250.3461.680
plotStatMap1.1630.3101.479
readConsensusFile0.0090.0030.013
readPopDef0.0060.0030.009
readSeaflow0.0870.0070.095
summarize1.4260.2261.654
summarizeFile1.0830.1381.228
validatePopDef0.0030.0020.005
writeSeaflow 0.103 0.01330.117