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Package 90/294HostnameOS / ArchBUILDCHECKBUILD BIN
flowClust 1.8.1
Raphael Gottardo
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/flowClust
Last Changed Rev: 37108 / Revision: 38965
Last Changed Date: 2009-02-03 15:13:48 -0800 (Tue, 03 Feb 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: flowClust
Version: 1.8.1
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes flowClust_1.8.1.tar.gz
StartedAt: 2009-04-18 18:45:01 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:46:44 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 103.3 seconds
RetCode: 0
Status: OK
CheckDir: flowClust.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/flowClust.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'flowClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowClust' version '1.8.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowClust' can be installed ... 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 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating flowClust-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating flowClust-manual.tex ... OK
* checking flowClust-manual.tex using pdflatex ... OK

flowClust.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/flowClust.Rcheck


---------- Making package flowClust ------------

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

  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making BoxCox.d from BoxCox.c
making flowClust.d from flowClust.c
making flowClustGaussian.d from flowClustGaussian.c
making ranMVNT.d from ranMVNT.c
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include   -Ie:/biocbld/bbs-2.3-bioc/R/src/include -IC:/gsl/include  -O3 -Wall  -c BoxCox.c -o BoxCox.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include   -Ie:/biocbld/bbs-2.3-bioc/R/src/include -IC:/gsl/include  -O3 -Wall  -c flowClust.c -o flowClust.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include   -Ie:/biocbld/bbs-2.3-bioc/R/src/include -IC:/gsl/include  -O3 -Wall  -c flowClustGaussian.c -o flowClustGaussian.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include   -Ie:/biocbld/bbs-2.3-bioc/R/src/include -IC:/gsl/include  -O3 -Wall  -c ranMVNT.c -o ranMVNT.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include  -i flowClust_res.rc -o flowClust_res.o
gcc  -std=gnu99  -shared -s  -o flowClust.dll flowClust.def BoxCox.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust_res.o  -Le:/biocbld/bbs-2.3-bioc/R/bin -LC:/gsl/bin -lgsl -lgslcblas -lm   -lR
Info: resolving _gsl_root_fsolver_brent by linking to __imp__gsl_root_fsolver_brent (auto-importc:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/ld.exe: warning: auto-importing has been activated without --enable-auto-import specified on the command line.
This should work unless it involves constant data structures referencing symbols from auto-imported DLLs.)

  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package flowClust for lazy loading
Loading required package: mnormt
Loading required package: mclust
Loading required package: ellipse
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)'.

Loading required package: flowCore
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
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
Loading required package: ks

Attaching package: 'flowCore'


	The following object(s) are masked from package:stats :

	 alias,
	 filter 

Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "Ulist" is defined (with package slot "rrcov") but no metadata object found to revise subclass information---not exported?  Making a copy in package "flowClust"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "Uvector" is defined (with package slot "rrcov") but no metadata object found to revise subclass information---not exported?  Making a copy in package "flowClust"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'flowClust'
     Formats: text html latex example chm 
  Map                               text    html    latex   example chm
  SimulateMixture                   text    html    latex   example chm
  Subset                            text    html    latex           chm
  box                               text    html    latex   example chm
  density                           text    html    latex   example chm
  dmvt                              text    html    latex           chm
  flowClust-internal                text    html    latex           chm
  flowClust-package                 text    html    latex           chm
  flowClust                         text    html    latex   example chm
  hist                              text    html    latex   example chm
  miscellaneous                     text    html    latex   example chm
  plot.flowClust                    text    html    latex   example chm
  plot.flowCore                     text    html    latex           chm
  plot.flowDens                     text    html    latex           chm
  rbox                              text    html    latex           chm
  rituximab                         text    html    latex           chm
  ruleOutliers                      text    html    latex   example chm
  show.flowClust                    text    html    latex           chm
  show.tmixFilter                   text    html    latex           chm
  split                             text    html    latex           chm
  summary                           text    html    latex           chm
  tmixFilter                        text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\flowClust.Rcheck\00_pkg_src\flowClust\chm\flowClust.chm


Compile time: 0 minutes, 0 seconds
23	Topics
272	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\flowClust.Rcheck\00_pkg_src\flowClust\chm\flowClust.chm, 56,900 bytes
Compression decreased file by 84,434 bytes.
  adding MD5 sums

* DONE (flowClust)