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Package 166/479HostnameOS / ArchBUILDCHECKBUILD BIN
flowWorkspace 0.99.11
Greg Finak
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace
Last Changed Rev: 56181 / Revision: 56603
Last Changed Date: 2011-06-14 17:49:10 -0700 (Tue, 14 Jun 2011)
wilson2 Linux (openSUSE 11.4) / 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 [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

Package: flowWorkspace
Version: 0.99.11
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowWorkspace_0.99.11.tar.gz
StartedAt: 2011-07-07 03:57:02 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:00:29 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 207.4 seconds
RetCode: 0
Status:  OK  
CheckDir: flowWorkspace.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/flowWorkspace.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '0.99.11'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'multicore' 'Rmpi' 'ncdf4'
* checking if this is a source package ... OK
* checking whether package 'flowWorkspace' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
writeGatesToNetCDF: no visible global function definition for
  'ncdim_def'
writeGatesToNetCDF: no visible global function definition for
  'ncvar_def'
writeGatesToNetCDF: no visible global function definition for
  'nc_create'
writeGatesToNetCDF: no visible global function definition for
  'ncvar_put'
writeGatesToNetCDF: no visible global function definition for
  'nc_close'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'run-all.R'
 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

flowWorkspace.Rcheck/00install.out:

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"       -O2 -Wall  -std=gnu99   -O2 -Wall  -std=gnu99 -c bitOps.c -o bitOps.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"       -O2 -Wall  -std=gnu99   -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"       -O2 -Wall  -std=gnu99   -O2 -Wall  -std=gnu99 -c netCDF.c -o netCDF.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o flowWorkspace.dll tmp.def bitOps.o init.o netCDF.o -lm -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/x64
** R
** inst
** preparing package for lazy loading
Loading required package: graph

Attaching package: 'XML'

The following object(s) are masked from 'package:graph':

    addNode

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

Attaching package: 'flowCore'

The following object(s) are masked from 'package:stats':

    alias, filter

Loading required package: lattice
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: grid
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
Creating a generic function for "lapply" from package "base" in package "flowWorkspace"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'flowWorkspace.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (flowWorkspace)

flowWorkspace.Rcheck/flowWorkspace-Ex.timings:

nameusersystemelapsed
GatingHierarchy-class31.32 1.0233.06
GatingSet-class27.41 0.5027.91
closeWorkspace000
ellipsoidGate2FlowJoVertices0.020.000.01
execute000
exportAsFlowJoXML000
flowJoWorkspace-class0.060.000.06
flowWorkspace2flowCore000
getBoundaries000
getChildren000
getCompensationMatrices000
getData000
getDimensions000
getGate000
getIndices000
getKeywords000
getNodes000
getParent000
getPopStats000
getProp000
getSample000
getSampleGroups000
getSamples000
getTotal000
getTransformations000
openWorkspace000
parseWorkspace000
plot000
plotGate000
plotPopCV000
plotWf000