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Package 179/516HostnameOS / ArchBUILDCHECKBUILD BIN
flowWorkspace 1.0.1
Greg Finak
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/flowWorkspace
Last Changed Rev: 60371 / Revision: 61898
Last Changed Date: 2011-11-15 17:27:28 -0800 (Tue, 15 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: flowWorkspace
Version: 1.0.1
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowWorkspace_1.0.1.tar.gz
StartedAt: 2012-01-09 02:51:34 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 02:54:41 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 187.2 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 2.14.1 (2011-12-22)
* 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 '1.0.1'
* checking package namespace 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 if there is a namespace ... 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 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
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 compiled code ... 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 -mtune=core2   -O2 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2   -O2 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2   -O2 -Wall  -std=gnu99 -mtune=core2 -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
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import '.__C__character' when loading 'methods'
Warning in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning in fun(libname, pkgname) :
  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 in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning messages:
1: replacing previous import '.__C__character' when loading 'methods' 
2: In fun(libname, pkgname) :
  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-class27.63 0.9728.84
GatingSet-class20.58 0.7721.35
closeWorkspace000
ellipsoidGate2FlowJoVertices0.010.000.01
execute000
exportAsFlowJoXML000
flowJoWorkspace-class0.080.000.08
flowWorkspace2flowCore000
getBoundaries000
getChildren000
getCompensationMatrices000
getData000
getDimensions000
getGate000
getIndices000
getKeywords000
getNodes000
getParent000
getPopStats000
getProp000
getSample000
getSampleGroups000
getSamples000
getTotal000
getTransformations000
openWorkspace000
parseWorkspace000
plot000
plotGate000
plotPopCV000
plotWf000