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Package 224/658HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.11.0
Chris Berthiaume
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowPhyto
Last Changed Rev: 70343 / Revision: 74756
Last Changed Date: 2012-10-09 08:57:59 -0700 (Tue, 09 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / 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 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: flowPhyto
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.11.0.tar.gz
StartedAt: 2013-03-24 05:05:23 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 05:09:27 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 244.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowPhyto.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowPhyto' can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from 'inst/doc' ... OK
* checking examples ... [90s/122s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        35.902  1.843  38.205
plotCruiseStats 10.257  0.919  11.066
censusFile       6.729  0.464   8.155
writeSeaflow     0.125  0.012  30.138
* 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-2.12-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

flowPhyto.Rcheck/00install.out:

* installing *source* package 'flowPhyto' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'flowPhyto.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS0.0060.0020.007
CHANNEL.CLMNS.SM0.2170.0020.219
EVT.HEADERS0.0060.0010.006
POP.DEF0.0160.0010.019
REPO.PATH0.0100.0000.011
census3.5190.0703.632
censusFile6.7290.4648.155
classify2.5140.2562.794
classifyFile2.3320.1682.661
cleanupLogs0.0030.0050.009
clearOutputs0.0200.0480.075
combineCensusFiles0.0160.0090.025
combineSdsFiles0.0200.0090.030
consensus1.7280.0261.762
consensusFile1.8020.0492.072
createResamplingScheme0.0250.0060.031
filter0.1920.0130.207
filterFile3.1770.3643.558
getCruiseFiles0.0150.0170.032
getCruisePath0.0060.0070.013
getFileNumber0.0070.0080.015
joinSDS0.2490.0160.267
pipeline35.902 1.84338.205
plotCruiseStats10.257 0.91911.066
plotCytogram2.5830.2872.886
plotLatLongMap1.8000.2422.059
plotStatMap1.7640.2111.983
readConsensusFile0.0220.0190.042
readPopDef0.0120.0070.018
readSeaflow0.120.010.13
summarize2.1930.1272.331
summarizeFile1.4880.0711.634
validatePopDef0.0080.0070.016
writeSeaflow 0.125 0.01230.138