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Package 161/463HostnameOS / ArchBUILDCHECKBUILD BIN
flowWorkspace 0.99.9
Greg Finak
Snapshot Date: 2011-06-02 07:21:07 -0700 (Thu, 02 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace
Last Changed Rev: 55821 / Revision: 55954
Last Changed Date: 2011-05-25 04:16:37 -0700 (Wed, 25 May 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 (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: flowWorkspace
Version: 0.99.9
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_0.99.9.tar.gz
StartedAt: 2011-06-02 14:37:39 -0700 (Thu, 02 Jun 2011)
EndedAt: 2011-06-02 14:42:20 -0700 (Thu, 02 Jun 2011)
EllapsedTime: 281.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowWorkspace.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/flowWorkspace.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘0.99.9’
* checking package name space information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘flowWorkspace.pdf’ from 1590Kb to 429Kb
  consider running tools::compactPDF() on these files
* 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’ ...
checking searching for non-standard locations of system libraries... /opt/local
done
checking for gcc... gcc-4.2 -arch i386 -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -arch i386 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for nc_def_compound in -lnetcdf... no
configure: WARNING: --with-netcdf was given, but test for netcdf failed
configure: WARNING: Package should still build but you won't have netcdf functionality
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating R/AllMethods.R
config.status: creating R/ncdfFlowSet-functions.R
config.status: creating src/Makevars
config.status: creating src/netCDF.c
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include   -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC  -g -O2 -c bitOps.c -o bitOps.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include   -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC  -g -O2 -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include   -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC  -g -O2 -c netCDF.c -o netCDF.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowWorkspace.so bitOps.o init.o netCDF.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/i386
** 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 1.3-00)

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
Creating a new generic function for "lapply" in "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 1.3-00)

* DONE (flowWorkspace)

flowWorkspace.Rcheck/flowWorkspace-Ex.timings:

nameusersystemelapsed
GatingHierarchy-class38.669 4.75743.850
GatingSet-class34.257 4.66439.721
closeWorkspace0.0000.0010.000
ellipsoidGate2FlowJoVertices0.0190.0010.021
execute0.0010.0000.001
exportAsFlowJoXML0.0010.0000.001
flowJoWorkspace-class0.1010.0120.117
flowWorkspace2flowCore0.0040.0010.005
getBoundaries0.0000.0010.001
getChildren0.0000.0000.001
getCompensationMatrices000
getData0.0010.0000.000
getDimensions0.0010.0000.001
getGate0.0010.0000.000
getIndices0.0010.0000.000
getKeywords0.0000.0000.001
getNodes000
getParent0.0000.0010.000
getPopStats0.0010.0000.000
getProp0.0000.0010.001
getSample0.0000.0000.001
getSampleGroups0.0000.0010.001
getSamples0.0010.0000.001
getTotal0.0000.0000.001
getTransformations000
openWorkspace000
parseWorkspace0.0000.0000.001
plot0.0000.0000.001
plotGate000
plotPopCV000
plotWf000