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BioC 2.12: CHECK report for flowPhyto on moscato2

This page was generated on 2013-10-09 09:38:51 -0700 (Wed, 09 Oct 2013).

Package 227/671HostnameOS / ArchBUILDCHECKBUILD BIN
flowPhyto 1.12.1
Chris Berthiaume
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/flowPhyto
Last Changed Rev: 81079 / Revision: 81334
Last Changed Date: 2013-10-02 11:05:02 -0700 (Wed, 02 Oct 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: flowPhyto
Version: 1.12.1
Command: rm -rf flowPhyto.buildbin-libdir && mkdir flowPhyto.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPhyto.buildbin-libdir flowPhyto_1.12.1.tar.gz >flowPhyto-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=flowPhyto.buildbin-libdir --install="check:flowPhyto-install.out" --force-multiarch --no-vignettes --timings flowPhyto_1.12.1.tar.gz && mv flowPhyto.buildbin-libdir/* flowPhyto.Rcheck/ && rmdir flowPhyto.buildbin-libdir
StartedAt: 2013-10-09 02:07:32 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:13:43 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 370.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowPhyto.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/flowPhyto.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.12.1'
* 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 whether package 'flowPhyto' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'library' or 'require' calls not declared from:
  'MASS' 'RSQLite' 'grid' 'sm'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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'
.heatmap.2: no visible global function definition for 'invalid'
.heatmap.2: no visible global function definition for 'heatmap.2.key'
.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'
dbWriteTable2: no visible binding for global variable 'db.nchars'
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'
hyperplot: no visible binding for global variable 'out'
plotCruiseStats: no visible binding for global variable 'resamp'
plotCytogram: no visible binding for global variable 'pop'
spie: no visible global function definition for 'grid.newpage'
spie: no visible global function definition for 'pushViewport'
spie: no visible global function definition for 'viewport'
spie: no visible global function definition for 'grid.layout'
spie: no visible global function definition for 'dataViewport'
spie: no visible global function definition for 'grid.circle'
spie: no visible global function definition for 'gpar'
spie: no visible global function definition for 'grid.polygon'
spie: no visible global function definition for 'grid.rect'
spie: no visible global function definition for 'stringWidth'
spie: no visible global function definition for 'stringHeight'
spie: no visible global function definition for 'grid.text'
spie: no visible global function definition for 'grid.lines'
spie: no visible global function definition for 'unit'
spie: no visible global function definition for 'upViewport'
stats: no visible global function definition for 'recode'
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 ... WARNING
Undocumented code objects:
  'addFactLevs' 'bestBy' 'cmdArgsToVariables' 'dbWriteTable2' 'delist'
  'geomean' 'groupBy' 'heatmatrix' 'hyperplot' 'labsegs' 'leghead' 'm'
  'makeElipseCoords' 'mvlabs' 'nerge' 'nv' 'pad' 'parseArgString' 'pct'
  'pies' 'plotClock' 'raAddArms' 'raAddAxLabs' 'raAddSigLines' 'raPlot'
  'read.tab' 'regroup' 'rerowname' 'spie' 'sstable' 'stats' 'tab2df'
  'textplot' 'usr2lims' 'vennMatrix' 'violins' 'wjitter' 'write.delim'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... [116s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCruiseStats 12.96   0.84   14.12
censusFile       5.93   0.19    8.45
pipeline         0.11   0.05   29.53
writeSeaflow     0.13   0.01   30.14
** running examples for arch 'x64' ... [110s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotCruiseStats 8.47   0.61    9.39
censusFile      6.01   0.14    6.72
writeSeaflow    0.14   0.00   30.14
pipeline        0.09   0.02   31.90
* 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 were 2 warnings.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

flowPhyto.Rcheck/00install.out:


install for i386

* 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
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'

install for x64

* installing *source* package 'flowPhyto' ...
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'
* MD5 sums
packaged installation of 'flowPhyto' as flowPhyto_1.12.1.zip
* DONE (flowPhyto)