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BioC 2.13: CHECK report for flowPhyto on zin1

This page was generated on 2014-04-05 09:47:59 -0700 (Sat, 05 Apr 2014).

Package 257/750HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.14.0
Chris Berthiaume
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowPhyto
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: flowPhyto
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings flowPhyto_1.14.0.tar.gz
StartedAt: 2014-04-05 01:09:51 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:12:18 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 147.9 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/flowPhyto.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.0’
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘flowPhyto.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [49s/78s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pipeline        20.845  0.824  21.785
plotCruiseStats  5.281  0.244   5.244
writeSeaflow     0.068  0.000  30.101
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (flowPhyto)

flowPhyto.Rcheck/flowPhyto-Ex.timings:

nameusersystemelapsed
CHANNEL.CLMNS0.0000.0040.003
CHANNEL.CLMNS.SM0.0000.0000.003
EVT.HEADERS0.0040.0000.003
POP.DEF0.0080.0000.008
REPO.PATH0.0040.0000.002
census1.8360.0041.842
censusFile3.6560.2483.744
classify1.3320.0001.332
classifyFile0.5840.0040.598
cleanupLogs0.0000.0000.001
clearOutputs0.0000.0080.011
cmdArgsToVariables0.0000.0000.001
combineCensusFiles0.0080.0000.010
combineSdsFiles0.0120.0000.012
consensus1.1040.0041.111
consensusFile1.1800.0041.204
createResamplingScheme0.0200.0000.019
filter0.1120.0000.123
filterFile1.7800.2681.888
getCruiseFiles0.0080.0000.008
getCruisePath0.0080.0000.004
getFileNumber0.0040.0000.004
joinSDS0.1560.0000.156
pipeline20.845 0.82421.785
plotCruiseStats5.2810.2445.244
plotCytogram1.3200.0081.327
plotLatLongMap0.9200.0520.979
plotStatMap0.8960.0200.919
readConsensusFile0.0120.0000.011
readPopDef0.0080.0000.008
readSeaflow0.0640.0000.065
summarize1.1400.0121.155
summarizeFile0.8640.0080.873
validatePopDef0.0040.0000.005
writeSeaflow 0.068 0.00030.101