rflowcyt 1.11.0
N. LeMeur
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rflowcyt | | Last Changed Rev: 27847 / Revision: 29143 | | Last Changed Date: 2007-10-08 11:45:32 -0700 (Mon, 08 Oct 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/rflowcyt.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'rflowcyt/DESCRIPTION' ... OK
* this is package 'rflowcyt' version '1.11.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rflowcyt' 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 ... WARNING
Rd files without 'description':
FCSggobi-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 S4 methods:
generic '[<-' and siglist 'FCS,ANY,ANY'
generic '[<-' and siglist 'FCSmetadata,ANY,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
* creating rflowcyt-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/tests'
Running 'FCSclass-tests.R'
Running 'FCSgateclass-tests.R'
Running 'FCSmetadataclass-tests.R'
Running 'fluors.FCS.R'
Running 'read.FCS-tests.R'
Running 'runflowcytests-tests.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
Package natbib Warning: Citation `robin:2001' on page 2 undefined on input line
Package natbib Warning: Citation `robin:2001' on page 3 undefined on input line
Package natbib Warning: Citation `gasparetto:smith:2004' on page 15 undefined o
Package natbib Warning: Citation `gasparetto:smith:2004' on page 22 undefined o
Package natbib Warning: Citation `roe:hardy:2001' on page 34 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 41 undefined on input
Package natbib Warning: Citation `fried:fish:1998' on page 42 undefined on inpu
Package natbib Warning: Citation `roe:hardy:2001' on page 43 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 43 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 48 undefined
Package natbib Warning: Citation `baggerly:2001' on page 48 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 52 undefined
Package natbib Warning: Citation `baggerly:2001' on page 52 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
Package natbib Warning: Citation `robin:2001' on page 3 undefined on input line
Package natbib Warning: Citation `robin:2001' on page 4 undefined on input line
Package natbib Warning: Citation `gasparetto:smith:2004' on page 16 undefined o
Package natbib Warning: Citation `gasparetto:smith:2004' on page 23 undefined o
Package natbib Warning: Citation `roe:hardy:2001' on page 35 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 42 undefined on input
Package natbib Warning: Citation `fried:fish:1998' on page 43 undefined on inpu
Package natbib Warning: Citation `roe:hardy:2001' on page 44 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 44 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 49 undefined
Package natbib Warning: Citation `baggerly:2001' on page 49 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 53 undefined
Package natbib Warning: Citation `baggerly:2001' on page 53 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
* creating rflowcyt-manual.tex ... OK
* checking rflowcyt-manual.tex ... OK
WARNING: There were 2 warnings, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck
* Installing *source* package 'rflowcyt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
Loading required package: xtable
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: MASS
Loading required package: grid
Loading required package: hexbin
Loading required package: lattice
Loading required package: rfcdmin
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Version 0.13-1 (2007-12-03).
Type demo( spam) for some demos, help( Spam) for an overview of this library.
Attaching package: 'spam'
The following object(s) are masked _by_ .GlobalEnv :
.Spam
The following object(s) are masked from package:xtable :
display
Try help(fields) for an overview of this library
Loading required package: locfit
Loading required package: akima
locfit 1.5-4 2007-11-27
Loading required package: splancs
Loading required package: sp
Spatial Point Pattern Analysis Code in S-Plus
Version 2 - Spatial and Space-Time analysis
Loading required package: prada
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: RColorBrewer
Loading required package: rrcov
Loading required package: robustbase
Attaching package: 'robustbase'
The following object(s) are masked from package:survival :
heart
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: xgobi
** help
Note: removing empty section \description
Note: removing empty section \examples
Note: removing empty section \value
>>> Building/Updating help pages for package 'rflowcyt'
Formats: text html latex example
ContourScatterPlot text html latex example
FCS-class text html latex example
FCSgate-class text html latex example
FCSggobi-class text html latex
FCSmetadata-class text html latex example
FCSsummary-class text html latex example
FHCRC.HVTNFCS text html latex example
ImageParCoord text html latex example
KS.flowcytest text html latex example
MODE text html latex example
PercentPos.FCS text html latex example
ProbBin.FCS text html latex example
ProbBin.flowcytest text html latex example
ROC.FCS text html latex example
VRC.HVTNFCS text html latex example
WLR.flowcytest text html latex example
add.parallel.coordinates text html latex example
add.parallelCoordinates text html latex example
addParameter-methods text html latex
boxplot.FCS text html latex example
breakpoints.ProbBin text html latex example
checkvars-methods text html latex
coerce-FCSformat text html latex example
coerce-methods text html latex
convertS3toS4 text html latex example
createGate text html latex example
cytoSet-class text html latex example
dim.FCS-methods text html latex
emp.f text html latex example
equals-methods text html latex
extractGateHistory text html latex example
extractGatedData text html latex example
fcs.type text html latex example
fixvars-methods text html latex
fluors-methods text html latex
gate.IPC text html latex example
get.h text html latex example
get.num.modes text html latex example
get.p text html latex example
ggobi-methods text html latex
legend.CSP text html latex example
make.grid text html latex example
metaData-methods text html latex
pairs.CSP text html latex example
parallelCoordinates text html latex example
pkci2.flowcytest text html latex example
plot-methods text html latex
plot.ProbBin.FCS text html latex example
plot2sets.FCS text html latex example
plotECDF.FCS text html latex example
plotQA.FCS text html latex example
plotdensity.FCS text html latex example
plotvar.FCS text html latex example
print-methods text html latex
read.FCS text html latex example
read.series.FCS text html latex example
rect.box.idx text html latex example
rflowcyt-defunct text html latex
runflowcytests text html latex example
show-methods text html latex
showgate.FCS text html latex example
standard text html latex example
subset-methods text html latex
subset2-methods text html latex
subset2assign-methods text html latex
subsetassign-methods text html latex
summary-methods text html latex
summary.ProbBin.FCS text html latex example
xgobi.FCS text html latex example
** building package indices ...
* DONE (rflowcyt)