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Package 195/553HostnameOS / ArchBUILDCHECKBUILD BIN
flowWorkspace 1.2.0
Greg Finak
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/flowWorkspace
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: flowWorkspace
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_1.2.0.tar.gz
StartedAt: 2012-09-24 00:09:20 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:12:52 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 211.8 seconds
RetCode: 0
Status:  OK 
CheckDir: flowWorkspace.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/flowWorkspace.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* 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 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 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: includedChannel2ExcludedChannel.Rd:24-26: Dropping empty section \details
prepare_Rd: includedChannel2ExcludedChannel.Rd:36-38: Dropping empty section \note
prepare_Rd: includedChannel2ExcludedChannel.Rd:30-32: Dropping empty section \references
prepare_Rd: includedChannel2ExcludedChannel.Rd:42-44: Dropping empty section \seealso
prepare_Rd: includedGate2ExcludedGate.Rd:25-27: Dropping empty section \details
prepare_Rd: includedGate2ExcludedGate.Rd:37-39: Dropping empty section \note
prepare_Rd: includedGate2ExcludedGate.Rd:31-33: Dropping empty section \references
prepare_Rd: includedGate2ExcludedGate.Rd:43-45: Dropping empty section \seealso
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

flowWorkspace.Rcheck/00install.out:

* installing *source* package 'flowWorkspace' ...
checking searching for non-standard locations of system libraries... done
checking for gcc... gcc -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 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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_var_deflate in -lnetcdf... no
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
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c bitOps.c -o bitOps.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
gcc -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'flowWorkspace.Rnw' 
** testing if installed package can be loaded

* DONE (flowWorkspace)

flowWorkspace.Rcheck/flowWorkspace-Ex.timings:

nameusersystemelapsed
GatingHierarchy-class22.023 2.74324.977
GatingSet-class19.794 2.40922.310
closeWorkspace0.0010.0000.000
ellipsoidGate2FlowJoVertices0.0170.0000.017
execute0.0010.0000.000
exportAsFlowJoXML0.0000.0000.001
flowJoWorkspace-class0.1100.0140.125
flowWorkspace2flowCore0.0030.0030.006
getBoundaries000
getChildren0.0010.0000.000
getCompensationMatrices0.0000.0000.001
getData0.0000.0010.001
getDimensions0.0010.0000.000
getGate0.0000.0000.001
getIndices000
getKeywords0.0000.0000.001
getNodes000
getParent0.0000.0000.001
getPopStats0.0000.0010.000
getProp0.0000.0000.001
getSample000
getSampleGroups0.0000.0000.001
getSamples000
getTotal0.0010.0000.000
getTransformations000
includedChannel2ExcludedChannel0.0000.0010.000
includedGate2ExcludedGate000
openWorkspace000
parseWorkspace0.0010.0000.001
plot000
plotGate0.0000.0000.001
plotPopCV000
plotWf0.0000.0010.001