Package: flowWorkspace

Version: 1.0.1

Command: E:\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 03:11:42 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:14:30 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 168.2 seconds

RetCode: 0

Status:  OK

CheckDir: flowWorkspace.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/flowWorkspace.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-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

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

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


** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -O3 -Wall  -std=gnu99 -mtune=core2   -O3 -Wall  -std=gnu99 -mtune=core2 -c bitOps.c -o bitOps.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -O3 -Wall  -std=gnu99 -mtune=core2   -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -O3 -Wall  -std=gnu99 -mtune=core2   -O3 -Wall  -std=gnu99 -mtune=core2 -c netCDF.c -o netCDF.o
gcc -shared -s -static-libgcc -o flowWorkspace.dll tmp.def bitOps.o init.o netCDF.o -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/i386
** 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'
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:
replacing previous import '.__C__character' when loading 'methods' 

* DONE (flowWorkspace)

name	user	system	elapsed
GatingHierarchy-class	24.41	0.86	25.57
GatingSet-class	18.09	0.72	18.95
closeWorkspace	0	0	0
ellipsoidGate2FlowJoVertices	0.02	0.00	0.02
execute	0	0	0
exportAsFlowJoXML	0	0	0
flowJoWorkspace-class	0.06	0.00	0.06
flowWorkspace2flowCore	0	0	0
getBoundaries	0	0	0
getChildren	0	0	0
getCompensationMatrices	0	0	0
getData	0	0	0
getDimensions	0	0	0
getGate	0	0	0
getIndices	0	0	0
getKeywords	0	0	0
getNodes	0	0	0
getParent	0	0	0
getPopStats	0	0	0
getProp	0	0	0
getSample	0	0	0
getSampleGroups	0	0	0
getSamples	0	0	0
getTotal	0	0	0
getTransformations	0	0	0
openWorkspace	0	0	0
parseWorkspace	0	0	0
plot	0	0	0
plotGate	0	0	0
plotPopCV	0	0	0
plotWf	0	0	0