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 |
* 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
/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)