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Package 91/294HostnameOS / ArchBUILDCHECKBUILD BIN
flowCore 1.8.3
Nolwenn Le Meur
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/flowCore
Last Changed Rev: 38169 / Revision: 38965
Last Changed Date: 2009-03-24 17:53:21 -0700 (Tue, 24 Mar 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: flowCore
Version: 1.8.3
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes flowCore_1.8.3.tar.gz
StartedAt: 2009-04-18 17:22:00 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:25:40 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 220.5 seconds
RetCode: 0
Status: OK
CheckDir: flowCore.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/flowCore.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.8.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowCore' can be installed ... 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating flowCore-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating flowCore-manual.tex ... OK
* checking flowCore-manual.tex using pdflatex ... OK

flowCore.Rcheck/00install.out:

* Installing *source* package 'flowCore' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolytope.c -o inPolytope.o
inPolytope.c: In function 'inPolytope':
inPolytope.c:95: warning: suggest parentheses around comparison in operand of |
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 flowCore.so biexponential.o inPolygon.o inPolytope.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolytope.c -o inPolytope.o
inPolytope.c: In function 'inPolytope':
inPolytope.c:95: warning: suggest parentheses around comparison in operand of |
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolytope.c -o inPolytope.o
inPolytope.c: In function 'inPolytope':
inPolytope.c:95: warning: suggest parentheses around comparison in operand of |
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o   -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inPolytope.c -o inPolytope.o
inPolytope.c: In function 'inPolytope':
inPolytope.c:95: warning: suggest parentheses around comparison in operand of |
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
pcaPP 0.1-1 loaded
Scalable Robust Estimators with High Breakdown Point (version 0.5-01)
Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: rpanel
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Package `rpanel', version 1.0-5
type help(rpanel) for summary information
Loading required package: ks
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

** help
 >>> Building/Updating help pages for package 'flowCore'
     Formats: text html latex example 
  EHtrans-class                     text    html    latex   example
  GvHD                              text    html    latex
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  arcsinhTransform                  text    html    latex   example
  asinht-class                      text    html    latex   example
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Note: removing empty section \seealso in file 'characterOrTransformation-class.Rd'
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  gateActionItem-class              text    html    latex   example
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  hyperlog-class                    text    html    latex   example
  identifier-methods                text    html    latex   example
  invsplitscale-class               text    html    latex   example
  keyword-methods                   text    html    latex   example
  kmeansFilter                      text    html    latex   example
  linearTransform                   text    html    latex   example
  lnTransform                       text    html    latex   example
  logTransform                      text    html    latex   example
  logarithm-class                   text    html    latex   example
  logicalFilterResult-class         text    html    latex   example
  logicleTransform                  text    html    latex   example
  manyFilterResult-class            text    html    latex   example
  multipleFilterResult-class        text    html    latex   example
  norm2Filter-class                 text    html    latex   example
  normalization-class               text    html    latex
  normalizeActionItem-class         text    html    latex   example
  normalizeView-class               text    html    latex   example
  parameterFilter-class             text    html    latex
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Note: removing empty section \seealso in file 'parameters-class.Rd'
  parameters-class                  text    html    latex   example
  parameters-methods                text    html    latex   example
  polygonGate                       text    html    latex   example
Note: removing empty section \examples in file 'polytopeGate.Rd'
  polytopeGate                      text    html    latex
  quadGate                          text    html    latex   example
  quadratic-class                   text    html    latex   example
  quadraticTransform                text    html    latex   example
  randomFilterResult-class          text    html    latex
  ratio-class                       text    html    latex   example
  read.FCS                          text    html    latex   example
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  read.flowSet                      text    html    latex   example
  rectangleGate                     text    html    latex   example
  sampleFilter-class                text    html    latex   example
  scaleTransform                    text    html    latex   example
  setOperationFilter-class          text    html    latex
Note: removing empty section \seealso in file 'singleParameterTransform-class.Rd'
  singleParameterTransform-class    text    html    latex   example
  sinht-class                       text    html    latex   example
  spillover-flowSet                 text    html    latex
  split-methods                     text    html    latex   example
  splitScaleTransform               text    html    latex   example
  splitscale-class                  text    html    latex   example
  squareroot-class                  text    html    latex   example
  summarizeFilter-methods           text    html    latex
  timeFilter-class                  text    html    latex   example
  transform-class                   text    html    latex   example
  transformActionItem-class         text    html    latex   example
  transformFilter-class             text    html    latex   example
  transformList-class               text    html    latex   example
  transformMap-class                text    html    latex   example
Note: removing empty section \seealso in file 'transformReference-class.Rd'
  transformReference-class          text    html    latex   example
  transformView-class               text    html    latex   example
Note: removing empty section \seealso in file 'transformation-class.Rd'
  transformation-class              text    html    latex   example
  truncateTransform                 text    html    latex   example
  unitytransform-class              text    html    latex   example
  view-class                        text    html    latex   example
  workFlow-class                    text    html    latex   example
** building package indices ...
* DONE (flowCore)