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Package 74/251HostnameOS / ArchBUILDCHECKBUILD BIN
flowCore 1.5.7
Nolwenn Le Meur
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore
Last Changed Rev: 29112 / Revision: 29143
Last Changed Date: 2007-12-08 23:02:01 -0800 (Sat, 08 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  WARNINGS  OK 
Package: flowCore
Version: 1.5.7
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check flowCore_1.5.7.tar.gz
StartedAt: 2007-12-11 05:59:50 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 06:06:21 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 390.6 seconds
RetCode: 0
Status: WARNINGS
CheckDir: flowCore.Rcheck
Warnings: 3

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/flowCore.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.5.7'
* 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 ... WARNING
Found the following significant warnings:
  Warning: argument in method definition changed from (e1) to (x)
See '/loc/home/biocbuild/bbs-2.2-bioc/meat/flowCore.Rcheck/00install.out' for details.
* 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 ... NOTE
read.FCS: no visible binding for global variable ‘filname’
* checking Rd files ... WARNING
Rd files without 'description':
  setOperationFilter-class.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  curv1Filter curv2Filter
Undocumented S4 classes:
  curv1Filter curv2Filter
Undocumented S4 methods:
  generic '%in%' and siglist 'flowFrame,curv1Filter'
  generic '%in%' and siglist 'flowFrame,curv2Filter'
  generic 'sampleNames<-' and siglist 'flowSet,ANY'
  generic 'show' and siglist 'curv1Filter'
  generic 'show' and siglist 'curv2Filter'
  generic 'split' and siglist 'flowSet,list,ANY'
  generic 'split' and siglist 'flowSet,factor,ANY'
  generic 'split' and siglist 'flowSet,numeric,ANY'
  generic 'split' and siglist 'flowSet,character,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './HowTo-flowCore.tex' ...
Package natbib Warning: Citation `Gasparetto2004' on page 1 undefined on input 
Package natbib Warning: Citation `Brazma2001' on page 2 undefined on input line
Package natbib Warning: Citation `Brazma2001' on page 2 undefined on input line
Package natbib Warning: Citation `Chicurel2002' on page 2 undefined on input li
Package natbib Warning: Citation `Boguski2003' on page 2 undefined on input lin
Package natbib Warning: Citation `Keeney2004' on page 2 undefined on input line
Package natbib Warning: Citation `Bagwell2004' on page 2 undefined on input lin
Package natbib Warning: Citation `Braylan2004' on page 2 undefined on input lin
Package natbib Warning: Citation `Parks1997' on page 2 undefined on input line 
Package natbib Warning: Citation `Suni2003' on page 2 undefined on input line 6
Package natbib Warning: Citation `LeMeur2006' on page 2 undefined on input line
Package natbib Warning: Citation `Spidlen2006' on page 2 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './HowTo-flowCore.tex' ...
Package natbib Warning: Citation `Gasparetto2004' on page 1 undefined on input 
Package natbib Warning: Citation `Brazma2001' on page 2 undefined on input line
Package natbib Warning: Citation `Brazma2001' on page 2 undefined on input line
Package natbib Warning: Citation `Chicurel2002' on page 2 undefined on input li
Package natbib Warning: Citation `Boguski2003' on page 2 undefined on input lin
Package natbib Warning: Citation `Keeney2004' on page 2 undefined on input line
Package natbib Warning: Citation `Bagwell2004' on page 2 undefined on input lin
Package natbib Warning: Citation `Braylan2004' on page 2 undefined on input lin
Package natbib Warning: Citation `Parks1997' on page 2 undefined on input line 
Package natbib Warning: Citation `Suni2003' on page 2 undefined on input line 6
Package natbib Warning: Citation `LeMeur2006' on page 2 undefined on input line
Package natbib Warning: Citation `Spidlen2006' on page 2 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './HowTo-flowCore.tex' ...
* creating flowCore-manual.tex ... OK
* checking flowCore-manual.tex ... OK

WARNING: There were 3 warnings, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/flowCore.Rcheck/00check.log
for details

flowCore.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/flowCore.Rcheck
* Installing *source* package 'flowCore' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
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: rrcov
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 0.4-03)

Attaching package: 'rrcov'


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

	 biplot,
	 predict,
	 screeplot 

Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: misc3d
Loading required package: rgl
Warning: argument in method definition changed from (e1) to (x)
Creating a new generic function for "colnames" in "flowCore"
Creating a new generic function for "colnames<-" in "flowCore"
Creating a new generic function for "nrow" in "flowCore"
Creating a new generic function for "ncol" in "flowCore"
** help
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \description
 >>> Building/Updating help pages for package 'flowCore'
     Formats: text html latex example 
  GvHD                              text    html    latex
  KmeansFilter                      text    html    latex   example
  Subset-methods                    text    html    latex   example
  arcsinhTransform                  text    html    latex   example
  biexponentialTransform            text    html    latex   example
  coerce                            text    html    latex   example
  compensate                        text    html    latex   example
  concreteFilter-class              text    html    latex
  each_col                          text    html    latex   example
  ellipsoidGate                     text    html    latex   example
  expressionFilter-class            text    html    latex
  filter-and-methods                text    html    latex
  filter-class                      text    html    latex
  filter-in-methods                 text    html    latex
  filter-on-methods                 text    html    latex   example
  filter                            text    html    latex   example
  filterDetails-methods             text    html    latex
  filterReference-class             text    html    latex
  filterResult-class                text    html    latex   example
  filterSet-class                   text    html    latex   example
  flowFrame-class                   text    html    latex
  flowSet-class                     text    html    latex   example
  flowSet                           text    html    latex
  fsApply                           text    html    latex   example
  identifier                        text    html    latex   example
  keyword-methods                   text    html    latex   example
  linearTransform                   text    html    latex   example
  lnTransform                       text    html    latex   example
  logTransform                      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
  parameterFilter-class             text    html    latex
  parameters                        text    html    latex   example
  print.filterSummary               text    html    latex   example
  quadraticTransform                text    html    latex   example
  randomFilterResult-class          text    html    latex
  read.FCS                          text    html    latex   example
  read.FCSheader                    text    html    latex   example
  read.flowSet                      text    html    latex   example
  rectangleGate                     text    html    latex   example
  sampleFilter-class                text    html    latex   example
  sampleFilter                      text    html    latex   example
  scaleTransform                    text    html    latex   example
  setOperationFilter-class          text    html    latex
  spillover-flowSet                 text    html    latex
  splitScaleTransform               text    html    latex   example
  transform-class                   text    html    latex   example
  transformFilter-class             text    html    latex   example
  transformList-class               text    html    latex   example
  transformMap-class                text    html    latex   example
  truncateTransform                 text    html    latex   example
** building package indices ...
* DONE (flowCore)